diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml new file mode 100644 index 00000000..c880dca1 --- /dev/null +++ b/.github/workflows/codeql.yml @@ -0,0 +1,42 @@ +name: "CodeQL" + +on: + push: + branches: [ "main", "gh-pages", "release" ] + pull_request: + branches: [ "main" ] + schedule: + - cron: "59 14 * * 5" + +jobs: + analyze: + name: Analyze + runs-on: ubuntu-latest + permissions: + actions: read + contents: read + security-events: write + + strategy: + fail-fast: false + matrix: + language: [ javascript, python ] + + steps: + - name: Checkout + uses: actions/checkout@v3 + + - name: Initialize CodeQL + uses: github/codeql-action/init@v2 + with: + languages: ${{ matrix.language }} + queries: +security-and-quality + + - name: Autobuild + uses: github/codeql-action/autobuild@v2 + if: ${{ matrix.language == 'javascript' || matrix.language == 'python' }} + + - name: Perform CodeQL Analysis + uses: github/codeql-action/analyze@v2 + with: + category: "/language:${{ matrix.language }}" diff --git a/.zenodo.json b/.zenodo.json index b36b3818..634d5e79 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -12,7 +12,7 @@ "name": "Andrew Jesaitis" }, { - "name": "bamiwoaluko" + "name": "Bamiwo Aluko" }, { "orcid": "https://orcid.org/0000-0002-6206-4638", diff --git a/AUTHORS.md b/AUTHORS.md index 49ca6978..c5c4d8e6 100644 --- a/AUTHORS.md +++ b/AUTHORS.md @@ -1,7 +1,7 @@ Thank you to the following contributors (in alphabetical order by user name): * Alain Domissy (@alaindomissy) * Andrew Jesaitis (@andrewjesaitis) -* @bamiwoaluko +* Bamiwo Aluko (@bamiwoaluko) * Benjamin Carr (@BenjaminHCCarr) * Michele Mastropietro (@elehcim) * Emannuel Fernandes de Oliveira Carvalho (@emannuelOC) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 0646b614..559a0293 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -106,12 +106,12 @@ The `dot` program from Graphviz is needed to render some of the diagrams. * For Debian/Ubuntu users: ```bash -sudo apt get install graphviz +sudo apt-get install graphviz ``` * For non-Debian/Ubuntu users, follow the directions at [the GraphViz download site](https://graphviz.org/download). ```bash # Create and activate a virtual environment -python -m venv venv +python3 -m venv venv source venv/bin/activate # update the version of pip, setuptools, and wheel (venv) pip install -U pip setuptools wheel @@ -119,12 +119,16 @@ source venv/bin/activate (venv) pip install ".[all]" # Create the HTML to visualize locally (venv) make html -(venv) open _build/index.html +(venv) open _build/html/index.html # Or you can start a serve that watches for local file changes (venv) make watch # Open in your browser ``` +You can use `udocker` or any other Docker compatible engine to build the +user guide, by setting the following environment variable: +`CWLTOOL_OPTIONS=--udocker`, or `CWLTOOL_OPTIONS=--podman` for Podman, or `CWLTOOL_OPTIONS=--singularity` for Singularity/Apptainer. + > NOTE: When you modify the packages installed with apt or pip, please verify > if the change needs to be applied to either or to both of CI and readthedocs. > ReadTheDocs builds and deploys previews. CI builds and deploys production @@ -148,7 +152,10 @@ are still working after the change. Use “tool description” not “tool wrapper” for describing the first argument given to the `cwl-runner` or `cwltool` commands. -### Code examples + +### Code Examples + +All CWL documents should be version 1.2 unless there is a very good reason otherwise. To include code into a Markdown file you have two options. For external files use the following command: @@ -182,6 +189,34 @@ If you are having trouble with links to sections or code blocks, it might be due to duplicated sections, or to spaces or other characters. To preview the generated links, use the `myst-anchors` tool. +### Troubleshooting + +General advice for troubleshooting is to increase the verbosity of Sphinx +logs. When using `make`, change your command to the following pattern: +`make SPHINXOPTS="-vvv" html`. Or if you are using `sphinx-build`, then +use the following: `sphinx-build -vvv -b html src build/`. + +It is also worth removing build directories and files such as `_build`, `build`, +and [`~/.cache/salad`](https://github.com/common-workflow-language/user_guide/issues/268#issuecomment-1276068865). +You may want to start afresh with a new Python virtual environment, +installing the dependencies from scratch. + +If running `make html` or `make watch` appears to run fine but [gets stuck +](https://github.com/common-workflow-language/user_guide/issues/268) at some +part of the process (`10%`, `33%`, `57%`, etc.) for longer than 2-5 minutes +you may have to try the following: + +1. Check if the Python dependencies installed in your Python virtual environment + have updates available (you can re-create the virtual environment, use `--upgrade` + for `pip`, or manually verify in PyPI and `pip`). +2. Use `top` or `htop` to find out if there is any `cwltool` command running. Then + try running that command individually to see what is the error message. +3. Upgrade your version of `docker` if you have [an error message]( + https://github.com/docker/compose/issues/8121#issuecomment-806055733) similar to + `docker: Failed to create the container ID file: open /tmp/....cid: no such file or directory.`. +4. Try using `udocker` instead of `docker`, by using `pip` to install it, and setting + `CWLTOOL_OPTIONS` to `--udocker`. + ## Other Resources General discussion of [Common Workflow Language][cwl-site] project diff --git a/LICENSE.md b/LICENSE.md index d3eb47a0..75596a51 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -16,9 +16,9 @@ You are free: for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the -license terms. +license terms: + -Under the following terms: * **Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow @@ -28,16 +28,14 @@ Under the following terms: so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. -**No additional restrictions**---You may not apply legal terms or +* **No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that: -Notices: - -* You do not have to comply with the license for elements of the + * You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation. -* No warranties are given. The license may not give you all of the + * No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material. @@ -55,7 +53,7 @@ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. -## Trademark + [cc-by-human]: https://creativecommons.org/licenses/by/4.0/ diff --git a/Makefile b/Makefile index 9f6459ec..c4627689 100644 --- a/Makefile +++ b/Makefile @@ -3,7 +3,7 @@ # You can set these variables from the command line, and also # from the environment for the first two. -SPHINXOPTS = "-W" +#SPHINXOPTS = # was "-W" (turn warnings into errors) SPHINXBUILD = sphinx-build SOURCEDIR = src BUILDDIR = _build @@ -33,7 +33,7 @@ watch: clean ## unittest-examples : unittest-examples: - cd src/_includes/cwl; cwltest --test=conformance-test.yml --tool=${RUNNER} + cd src/_includes/cwl; cwltest --test=cwl_tests.yml --tool=${RUNNER} ## check-json : check-json: @@ -42,6 +42,10 @@ check-json: container-pull: for container in $$(git grep dockerPull $$(git ls-files *.cwl) | awk '-F: ' '{print $$3}'); do docker pull $${container}; done +update_translations: gettext + sphinx-intl update -p _build/gettext + + .PHONY: help clean watch unittest-examples check-json Makefile # Catch-all target : route all unknown targets to Sphinx using the new diff --git a/README.md b/README.md index de079218..d6817cc9 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,8 @@ [![Syntax Check](https://app.travis-ci.com/common-workflow-language/user_guide.svg?branch=main)](https://app.travis-ci.com/common-workflow-language/user_guide) +[![Translation status](https://hosted.weblate.org/widgets/commonwl/-/user-guide/svg-badge.svg)](https://hosted.weblate.org/engage/commonwl/) + This is the source of the official user guide for the Common Workflow Language standards. Releases are published at from the `release` branch. diff --git a/cwl/sphinx/runcmd.py b/cwl/sphinx/runcmd.py index ff8bb245..b4ea08de 100644 --- a/cwl/sphinx/runcmd.py +++ b/cwl/sphinx/runcmd.py @@ -40,10 +40,13 @@ class Singleton(_Singleton("SingletonMeta", (object,), {})): class CMDCache(Singleton): cache = {} + exclude_cache_cmd = {hash("cat output.txt")} def get(self, cmd, working_directory): h = hash(cmd) - if h in self.cache: + if h in self.exclude_cache_cmd: + return run_command(cmd, working_directory) + elif h in self.cache: return self.cache[h] else: result = run_command(cmd, working_directory) diff --git a/locales/es/LC_MESSAGES/sphinx.po b/locales/es/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..2bdf9af4 --- /dev/null +++ b/locales/es/LC_MESSAGES/sphinx.po @@ -0,0 +1,30 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: 2023-01-26 13:55+0000\n" +"Last-Translator: Michael Crusoe \n" +"Language-Team: Spanish \n" +"Language: es\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" +"X-Generator: Weblate 4.16-dev\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 d65b012160e9455eb4d2628279fffc42 +msgid "Main navigation" +msgstr "Navegación principal" + +#: ../../src/_templates/sidebar-nav-bs.html:3 4b3441eb77f448daa60718b7bfa862db +msgid "Section Navigation" +msgstr "Sección Navegación" diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po new file mode 100644 index 00000000..ca09ccab --- /dev/null +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -0,0 +1,3774 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-27 16:02+0100\n" +"PO-Revision-Date: 2023-01-27 14:27+0000\n" +"Last-Translator: Michael Crusoe \n" +"Language: es\n" +"Language-Team: Spanish \n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../LICENSE.md:2 3eb955b4f3dd4c3188924b97ea6ab592 +msgid "Licenses" +msgstr "Licencias" + +#: ../../LICENSE.md:4 bf4480e7fff4460a87e8f43c11599f07 +msgid "Instructional Material" +msgstr "Material didáctico" + +#: ../../LICENSE.md:6 9e9eab12205d4e82b4fedca520370f4c +msgid "" +"All Common Workflow Language project instructional material and changes to " +"the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable summary " +"of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" +"[cc-by-legal]." +msgstr "" +"Todo el material instructivo del proyecto Common Workflow Language y los " +"cambios en la estructura también están disponibles bajo la [licencia " +"Creative Commons Attribution][cc-by-human]. Lo que sigue es un resumen " +"legible por humanos (y no un sustituto) del [texto legal completo de la " +"licencia CC BY 4.0][cc-by-legal]." + +#: ../../LICENSE.md:12 a8e98ad541c642e58e201afa625ec791 +msgid "You are free:" +msgstr "Usted es libre de:" + +#: ../../LICENSE.md:14 b4cb4bc4261347fcb0d2c8a93995ab76 +msgid "" +"to **Share**---copy and redistribute the material in any medium or format" +msgstr "" +"**Compartir**---copiar y redistribuir el material en cualquier medio o " +"formato" + +#: ../../LICENSE.md:15 d66dcbf95ccc41aaa53be523487ec913 +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "**Adaptar**---remezclar, transformar y construir a partir del material" + +#: ../../LICENSE.md:17 ca1c299a1b834b868bcdd4ca9f244696 +msgid "for any purpose, even commercially." +msgstr "para cualquier propósito, incluso comercialmente." + +#: ../../LICENSE.md:19 6133f79f93be4991a6f5290f72d1a63d +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the license " +"terms:" +msgstr "" +"La licenciante no puede revocar estas libertades en tanto usted siga los " +"términos de la licencia:" + +#: ../../LICENSE.md:24 2d6ce81add1043629b676187f890288c +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow Language " +"project, and, where practical, linking to https://www.commonwl.org/ ), " +"provide a [link to the license][cc-by-human], and indicate if changes were " +"made. You may do so in any reasonable manner, but not in any way that " +"suggests the licensor endorses you or your use." +msgstr "" +"**Atribución**---Usted debe dar crédito de manera adecuada(mencionando que " +"su trabajo se deriva de un trabajo que tiene «Copyright © The Common " +"Workflow Language Project» y, cuando sea práctico, con un enlace a https://" +"www.commonwl.org/ ), brindar un [enlace a la licencia][cc-by-human], e " +"indicar si se han realizado cambios. Puede hacerlo en cualquier forma " +"razonable, pero no de forma tal que sugiera que usted o su uso tienen el " +"apoyo de la licenciante." + +#: ../../LICENSE.md:32 f3f22597b6f845208a0cce3b3b2c8f5d +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything the " +"license permits. With the understanding that:" +msgstr "" +"**No hay restricciones adicionales**---No puede aplicar términos legales ni " +"medidas tecnológicas que restrinjan legalmente a otras a hacer cualquier uso " +"permitido por la licencia. Con el entendimiento de que:" + +#: ../../LICENSE.md:36 3cfedee64d4e46098a159cb2acdba4ef +msgid "" +"You do not have to comply with the license for elements of the material in " +"the public domain or where your use is permitted by an applicable exception " +"or limitation." +msgstr "" +"No tiene que cumplir con la licencia para elementos del materiale en el " +"dominio público o cuando su uso esté permitido por una excepción o " +"limitación aplicable." + +#: ../../LICENSE.md:39 c836a570faaf449d9716da5f75556627 +msgid "" +"No warranties are given. The license may not give you all of the permissions " +"necessary for your intended use. For example, other rights such as " +"publicity, privacy, or moral rights may limit how you use the material." +msgstr "" +"No se dan garantías. La licencia podría no darle todos los permisos que " +"necesita para el uso que tenga previsto. Por ejemplo, otros derechos como " +"publicidad, privacidad, o derechos morales pueden limitar la forma en que " +"utilice el material." + +#: ../../LICENSE.md:44 896f9966e5014e8a88b060be3063fe09 +msgid "Software" +msgstr "Software" + +#: ../../LICENSE.md:46 007f8613dc234c3fa8d5d92b18af0eb1 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the " +"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" +"Excepto cuando se indique lo contrario, los programas de ejemplo y otro " +"software proporcionado por el proyecto Common Workflow Language están " +"disponibles bajo la [licencia Apache 2.0][apache-2.0-license] aprobada por " +"la [OSI][osi]." + +#: ../../LICENSE.md:51 227bc635a06f49dbb771fd9b62157d00 +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." +msgstr "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." + +#: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 +#: 1861131d3df648ae9e74ce1c87f0be7b a2ffa927deb2451d95ec63528e8078dd +#: d6055d3f15604ce6940770c7b561d4c5 +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece of " +"software, tools and workflows described using CWL are portable across a " +"variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/episodes.md:5 ../../src/setup.md:5 +#: 38b062f219b34e08a46bd8f6525353ec 89e7e1dd05474344a1d929cb492e9caf +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 d3357ff3c8874e368aea0d6062ef6190 +msgid "" +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. Please use the new [Table of Contents](index.md#table-of-" +"contents) to browse the User Guide." +msgstr "" + +#: ../../src/faq.md:1 f2c4882e0e164c2b869e3eb969241061 +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 41099ab64e0544d894bd9e3af2718bda +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 bb6aff70534148fa8a4b01140f7be150 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 70ebc653b0d54d60a866edc0dbf56b57 +msgid "" +"This example demonstrates how to change the name of an input file as part of " +"a tool description. This could be useful when you are taking files produced " +"from another step in a workflow, and don't want to work with the default " +"names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 38b687f707d2438b85df08a445ab816f +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 d48422c020004ef084ca11e6229b5450 +msgid "" +"This example demonstrates how to change the name of an output file from the " +"default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 48765409ab9d48ccbcecceb46ddf2e91 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 a59b8acd72124e2c95d1905ae494d928 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 f36088ba90d24f9f9c7c1bd59deb6f49 +msgid "" +"The first method involves adding the folder containing your scripts to the " +"`PATH` environment variable. This allows you to run the shell script " +"directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 45ee965ee4a7494a8354b82208e2ab45 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 734cc1abe1c841ffac8d0895463d91fc +msgid "" +"After that, make the script executable with the command `chmod +x scriptname." +"sh`" +msgstr "" + +#: ../../src/faq.md:97 f01bc8c4d6134f0ea27dc7f5b39def24 +msgid "" +"Finally, modify your `PATH` to add the directory where your script is " +"located. (It is good practice to use `$HOME/bin` for storing your own " +"scripts)." +msgstr "" + +#: ../../src/faq.md:104 dd6fc2a04e3b476892f05bc5b746d0fa +msgid "" +"Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 e309eaad55144052866ce131eb80fd14 +msgid "" +"When you wish to share your work later, you can place your script in a " +"software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 f0d649a60a13404ebecd540789202b87 +msgid "" +"The second method involves including an input of `type: File` in the script " +"itself:" +msgstr "" + +#: ../../src/faq.md:135 e2b782f88d494de398af0c9002a3ccdc +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 b4a033731fcd4322bd2bb71c609a4cb7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 43a64810b12b4c7d82a5803c3b910fe5 +msgid "" +"Currently, `cwltool` can't cope with missing optional inputs if their input " +"binding makes use of `self`. Below is an example workaround for this, " +"pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 60f009e3714c405695da069204b196ea +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 98916ed9355842e49bef073430e10675 +msgid "" +"Below is an example showing how to specify different strings to be added to " +"a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 9b8f2d0b33db4bbc82aaf5836b6f7ed8 +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 a251693354d24bf0bda4938c8890090a +msgid "" +"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" +"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 f46740ac0acb473583facb9f7528d03c +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 7de1f9e3175b4c2ab156192f28fd3535 +msgid "" +"The input must be an array consisting of exactly one entry for each input " +"link. If \"merge_nested\" is specified with a single link, the value from " +"the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 225c6f08068e41f58eb62f99dc06210f +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 4e741f4e3bc74e10bd9568826e81c478 +msgid "" +"Or in other words: if the destination is of type `File[]` (an array of " +"`File`s) and the source is a single `File` then add " +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " +"add `linkMerge: merge_nested` under the appropriate `in` entry of the " +"destination step." +msgstr "" + +#: ../../src/faq.md:229 bfdb011cb81c4ef9b9e56b24f1e9ccd5 +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 09f385e325f942afaa3dd195c16a18d2 +msgid "" +"To make an input parameter optional, add a question mark to the type " +"declaration." +msgstr "" + +#: ../../src/faq.md:247 c5d087082bb2468483e7ccda3ca45a07 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 41e30b0224a0492f9047b4f320f39a23 +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 f06d073014a44f33a60d947a8c5b0e59 +msgid "" +"For command line flags that require a specific input as the argument an enum " +"type can be declared in CWL. **Specifying null here is known as long form " +"style. It does the same thing as the question mark on the other inputs.**" +msgstr "" + +#: ../../src/faq.md:267 2fb74cd1b41e4fdb81a8f9b3b6c84373 +msgid "" +msgstr "" + +#: ../../src/faq.md:268 09e19f34d0fd4e388d4939cbc2be3436 +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 1ecae448dfcf45a4ae0dd39bd011e449 +msgid "" +"For commandline flags that are either **mutually exclusive** or " +"**dependent** a special record type can be defined. You can also specify " +"null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 6df3d4e918cc4bccb823859ce07b197a +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 086db1a093e64caa88d958150accc19c +msgid "" +"To properly set fields in a record input type, you need to pass a dictionary " +"to the input to properly set the parameters. This is done by using inline " +"JavaScript and returning the dictionary with the key of the field you want " +"to set. The source field is set to indicate the input from the workflow to " +"be used as the value." +msgstr "" + +#: ../../src/faq.md:342 da77c818d8694ab99fb2eccf73083047 +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 254259509ed6462d8ebc296b5f811f44 +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 f7a44f76579d4709a61d2d61bc352b76 +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 d67278e99c684f488f1e3418e1c8c207 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 f5e35ee06cd24edf831589ebaa6193d2 +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 2ffb67e547c446499625a8db9a102da6 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 ee653ff9fefe4771b35e2e76199b536a +msgid "" +"For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "" + +#: ../../src/faq.md:371 02b1eb159e934fd692929f7c30319ddd +msgid "" +"If you can not avoid these dangerous characters, then pass `--relax-path-" +"checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 857024702f624885be706c405b7a088e +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 d664e30899bd463bb48d38adec318dd4 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 9f3957bbe205454e8bffc4b5caac5970 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 6ec3bbc6a1ca4e23b47f025f0732e609 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 3e727d79e65e4c6cb157550e80261c53 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 6e0705f4ab4b4e9093794cb4fccb6be9 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 0047d039317349679fb6a66d18ec8487 +msgid "" +"If it is not possible to change the input identifier, then you can use an " +"alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 8c39608ad0494bee9a4a422cbeb34387 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 7dac53bca8c14a3f9af75cb162cba4f9 +msgid "" +"The CWL standards are built around (optional) Docker format containers. The " +"reference runner and several other CWL implementations support running those " +"Docker format containers using the Singularity engine. Directly specifying a " +"Singularity format container is not part of the CWL standards." +msgstr "" + +#: ../../src/faq.md:450 ffcc38ff98324d71bfeb8d66d4901da7 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 0d7bf2cefe4a4e22b186bdf4d0ed793d +msgid "" +"You can use the --js-console option of cwltool, or " +"you can try creating a JavaScript or TypeScript project for your code, and " +"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" +"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + +#: ../../src/index.md:1 1506b4e7ee014a01bfdb067489501a9e +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 0ce058b5210d46a0b78eb78dbca07a9f +msgid "" +"This guide will introduce you to writing workflows using the [Common " +"Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " +"guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 3404c064950d453d8af446e8b6554cb6 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 1e239cad669648e48694eaf91284766a +msgid "" +"If you find that something is missing from this guide, or if you would like " +"to provide other feedback, file an Issue on the [project repository for this " +"guide][repo]. You can also suggest changes directly in a Pull Request by " +"clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 9dba2e06f1be4a50b1fabaaf216d02b4 +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 ba4074bbb69e4096a808001afaf2e0dc +msgid "" +"If you are a beginner user get started with the [Introduction](/introduction/" +"index.md) section. For advanced users the subsections of the [Topics](/" +"topics/index.md) have detailed information about the most common topics for " +"CWL." +msgstr "" + +#: ../../src/index.md:23 ad34a37bf4ec488bb825a34456f4fe8d +msgid "" +"The Table of Contents is displayed at the top menu and also on the left " +"sidebar. It also appears further down this page but with links to " +"subsections. The right sidebar contains links to the sections of each page, " +"and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 2bd8eb5957ed40f4a72a6b7408044c78 +msgid "Table of Contents" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:1 8bb0df5531474301a185f1ba375320df +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 653373e1f11e4f81ad561378854a71fc +msgid "" +"This section describes the basic concepts for users to get started on " +"working with Common Workflow Language (CWL) workflows. Readers are expected " +"to be familiar with workflow managers, YAML, and comfortable with following " +"instructions for the command-line. The other sections of the user guide " +"cover the same concepts, but in more detail. If you are already familiar " +"with CWL or you are looking for more advanced content, you may want to skip " +"this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 7766227bf91b48b2b9752b625e5a9084 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 032d414ac29740aa9041d89d0ebf70e6 +msgid "" +"The CWL specification is a document written and maintained by the CWL " +"community. The specification has different versions. The version covered in " +"this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 74e92eb0a4e64098b5aaf08d043e0641 +msgid "" +"The specification version can have up to three numbers separated by `.`s " +"(dots). The first number is the major release, used for backward-" +"incompatible changes like the removal of deprecated features. The second " +"number is the minor release, used for new features or smaller changes that " +"are backward-compatible. The last number is used for bug fixes, like typos " +"and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 baa40b445f3c409b9a3e10a85fa38bfd +msgid "" +"The model used for the specification version is called Semantic Versioning. " +"See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 648e94a9d368450dbdac706445254c9f +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 e9ae15124dcd408395fc67e16b50696a +msgid "" +"An implementation of the CWL specification is any software written following " +"what is defined in a version of the specification document. However, " +"implementations may not implement every aspect of the specification. CWL " +"implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 b1c864d6775048cab01eb3de641f6475 +msgid "" +"CWL is well suited for describing large-scale workflows in cluster, cloud " +"and high performance computing environments where tasks are scheduled in " +"parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 a05d24121e534d65947eb26e4dada5b7 +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: ace0388fd04845e79d31ec99a48a8a3f +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 70ecd37237e14ae19539f2bf692882ed +msgid "" +"A process is a computing unit that takes inputs and produces outputs. The " +"behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification " +"{{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 38121b4b00324bebb6499184b3dcb5c1 +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: e0c278f52e824673ac708885d985b7d2 +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: 6b4d0f0651cc46f5abf195b281967913 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 88bdc9e046e4487cb0eee3f1d4819e57 +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 12eed3ef7d444585b150bbdab0665bc8 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: dfc85226313d46f9868dc4de53546a69 +msgid "" +"A command-line tool is a wrapper for a command-line utility like `echo`, " +"`ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: f636b10c47734e589291de95443d8115 +msgid "" +"An expression tool is a wrapper for a JavaScript expression. It can be used " +"to simplify workflows and command-line tools, moving common parts of a " +"workflow execution into reusable JavaScript code that takes inputs and " +"produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: bb51025d04444dd5b16000d5d6a3f41a +msgid "" +"Operation is an abstract process that also takes inputs, produces outputs, " +"and can be used in a workflow. But it is a special operation not so commonly " +"used. It is discussed in the [Operations section](../topics/operations.md) " +"of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 93dbaa0aa2c6493ab22a937c6861fac4 +msgid "" +"The workflow is a process that contains steps. Steps can be other workflows " +"(nested workflows), command-line tools, or expression tools. The inputs of a " +"workflow can be passed to any of its steps, while the outputs produced by " +"its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: fcde5ef65ebf45a3b4b67eec993a1729 +msgid "" +"The CWL specification allows for implementations to provide extra " +"functionality and specify prerequisites to workflows through *requirements*. " +"There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: c8ff34ff5d3b4a508e8c291196d08067 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: fe25f15fc11c49ab827b884d081c3df0 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 2b93b6219142431ca748a404a56ced5d +msgid "" +"`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 0094b13b26014ba3be61769b422802f5 +msgid "" +"Some CWL runners may provide requirements that are not in the specification. " +"For example, GPU requirements are supported in `cwltool` through the " +"`cwltool:CUDARequirement` requirement, but it is not part of the " +"{{ cwl_version }} specification and may not be supported by other CWL " +"runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: 576a0778d3dd44f68cb241346f441660 +msgid "" +"Hints are similar to requirements, but while requirements list features that " +"are required, hints list optional features. Requirements are explained in " +"detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: 7d98949fe97744158fad81f41d780de9 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: fc142b791aa1434aa75b0782248de988 +msgid "" +"The FAIR principles have laid a foundation for sharing and publishing " +"digital assets, and in particular, data. The FAIR principles emphasize " +"machine accessibility and that all digital assets should be Findable, " +"Accessible, Interoperable, and Reusable. Workflows encode the methods by " +"which the scientific process is conducted and via which data are created. It " +"is thus important that workflows support the creation of FAIR data and " +"adhere to the FAIR principles. — [FAIR Computational Workflows](https://" +"workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: c3fc91ae3bae4e3db60e8271e95135a2 +msgid "" +"CWL has roots in \"make\" and many similar tools that determine order of " +"execution, based on dependencies between tasks. However, unlike \"make\", " +"CWL tasks are isolated, and you must be explicit about your inputs and " +"outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 8f097ae5ff6a4be0b7428345362dc55e +msgid "" +"The benefit of explicitness and isolation are flexibility, portability, and " +"scalability; tools and workflows described with CWL can transparently " +"leverage technologies such as Docker and be used with CWL implementations " +"from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 60c56fa6a67346d6966f0d841213e11b +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 7377b155e8694798994bbc911a3f3152 +#: 7699685836064bd89db530a9c1918865 7d187a209ebd4e3ba6c6aeb05743041a +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 3fcbf810c86f4cf7b8499de88147aa95 +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: e242228b6b3d440cbca8418050220267 +msgid "" +"The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 6e01963a01cb49e39692455256679bfc +msgid "" +"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: ed81ea2234b041c79449dcd20f886cb6 +msgid "" +"The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: e8e3996f6a894b4f9cc266b46cb8d756 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: 085e4d1a7a9744d2884f3003c64ca174 +msgid "" +"CWL Operations are covered in the [Operations](../topics/operations.md) " +"section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 dcd96950854f47a6ad4169320c1dab34 +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 c4d17eec31874bf1ae9b49d73537d86c +msgid "" +"This section will guide you through a short introduction to CWL, the " +"prerequisites for following this user guide, and some basic concepts that " +"are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 98a8bdfc7c91436d9cb46abbb7c19c57 +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 244a716e267540c782e627adaea3a413 +msgid "" +"The software and configurations listed in this section are prerequisites for " +"following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements focuses " +"on the CWL reference runner, `cwltool`. You can use another CWL-compatible " +"runner or workflow system, but the results and interface may look different " +"(though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 2cdf453d2c8b4e2ea50555ef0b7364e5 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 53643a4f190c412d9552d1908f408318 +msgid "" +"There are many implementations of the CWL standards. Some are complete CWL " +"runners, while others could be plug-ins or extensions to workflow engines. " +"We have a better explanation in the [Implementations](basic-concepts." +"md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 1df6c63de3914af68f758054fe6955f4 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 ceaa3a6bebab45a0907ee0cad01429a2 +msgid "" +"We recommend using an up-to-date operating system. You can choose any of the " +"following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 1506ac904c6345c5806704a0ccf235aa +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 a616213ed24e427bb91ee33cb21ec131 +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 a4e9ae38103843739f13c62befd21f3e +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 2cd231aac42c4a69a925cea369999a8b +msgid "" +"If you are using Windows, you will have to install the [Windows Subsystem " +"for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). " +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool/blob/main/README.rst#ms-windows-users) for details on " +"installing WSL2. Your operating system also needs internet access and a " +"recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 051d7cd7d3a94baa865d180afdd71688 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 1a93aaf5bd5e4862b15e0636b4478640 +msgid "" +"The first thing you will need for running CWL workflows is a CWL runner. " +"`cwltool` is a Python Open Source project maintained by the CWL community. " +"It is also the CWL reference runner, which means it must support everything " +"in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 edd0613118a2493c876652bdcb9e0fbf +msgid "" +"`cwltool` can be installed with `pip`. We recommend using a virtual " +"environment like `venv` or `conda`. The following commands will create and " +"activate a Python virtual environment using the `venv` module, and install " +"`cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 3448d215c2434866b8a4b340872ba81e +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 4c24d05f65794735b816024c78b63f1c +msgid "" +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool#install) for other ways to install `cwltool` with `apt` and " +"`conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 3167f4a2a8394feda1f848334be62022 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 3c4b67d62c9c4d658ccaafcd1977ec08 +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 30792f78348942e0acdde411342e8830 +msgid "" +"The `cwltool` command has an option to validate CWL tool and workflow " +"descriptions. This option will parse the CWL document, look for syntax " +"errors, and verify that the workflow descriptions are compliant with the CWL " +"standards. However, these actions will be performed without running the " +"document. To validate CWL workflows (or even a standalone command line tool " +"description like the above) pass the `--validate` option to the `cwltool` " +"command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 4473e41281fb4e738e4eb26c2d178934 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 548393974d4d4acc91738f9bc13a3a48 +msgid "" +"You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 2ab3963cf9504ec097eda2b14f3448c4 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 690882dcc29c48acbeb215a8be52eb9e +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 6c3ba51b1e9a4add9203d62cec6ebae9 +msgid "" +"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " +"runner. This simply means that the `cwl-runner` alias command can be invoked " +"independently, and is not reliant on a particular CWL runner program name. " +"Users can invoke `cwl-runner` instead of invoking a CWL runner like " +"`cwltool` directly. The `cwl-runner` is installed by a system administrator " +"or user to point to the preferred CWL implementation. This is convenient for " +"environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 b2360ef646854422ad6c0f90fa49306f +msgid "" +"The CWL community publishes a Python package with the name `cwlref-runner` " +"that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 c9fadfa85a2641378e99a462e8e8d940 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 abb8993ede4d4e479d88d2e848546f68 +msgid "" +"Now you can validate and run your workflow with the `cwl-runner` executable, " +"which will invoke `cwltool`. You should have the same results and output as " +"in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 ba0f7606e6174e53a8bf23c1ccd99250 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 dd2e10f43e8f498cb01de5faa4fccb70 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 e500e9c71c7042169c25b31f21a09142 +msgid "" +"Another way to execute `cwl-runner` is by invoking the file directly. For " +"that, the first thing you need to do is copy `true.cwl` workflow into a new " +"file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 d989516c873f4446bba005f42796b8b9 +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 e9d8610478094a98b5b5a0f568a315de +msgid "" +"Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 d6d8131f91b740189e56ab9d90bee55a +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 def7400a00e84070a4bd80c2367d3bde +msgid "" +"And finally, you can execute it directly in the command-line. On execution, " +"the program specified in the shebang (`cwl-runner`) will be used to execute " +"the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 564e7be94d254e52a6c44b234d6ddc63 +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 bb5fe42ddd814ad4ac1071c0b18f24c2 +msgid "" +"The *shebang* is the two-character sequence `#!` at the beginning of a " +"script. When the script is executable, the operating system will execute the " +"script using the executable specified after the shebang. It is considered a " +"good practice to use `/usr/bin/env ` rather than using a hard-" +"coded location, since `/usr/bin/env ` looks for the " +"`` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 53bb712a68cd49fca4db11e9e507c9a4 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 bdcf61cce5294e45a9f964628a8a66bd +msgid "" +"You can use any text editor with CWL, but for syntax highlighting we " +"recommend an editor with YAML support. Popular editors are Visual Studio " +"Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 28d33daee6e246c8a6d1382208e19c39 +msgid "" +"There are extensions for Visual Studio Code and WebStorm that provide " +"integration with CWL, and features such as customized syntax highlighting " +"and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 b071d7c87b7a4817b871085a652cd580 +msgid "" +"Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 97658a1b16874ba8b0bb748242d0da64 +msgid "" +"cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 6198aa6769b74ef0a2a1ba539789f3ee +msgid "" +"The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 0c17235a374e40099be37b9b8ac8f1f0 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 e3690e656b5a4348845c654689935a88 +msgid "" +"`cwltool` uses Docker to run tools, workflows, and workflow steps that " +"specify a software container. Follow the instructions in the Docker " +"documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 2db34e925a81422986ccb868463a7a42 +msgid "" +"You do not need to know how to write and build Docker containers. In the " +"rest of the user guide, we will use existing Docker images for running " +"examples, and to clarify the differences between the execution models with " +"and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 d677fb155b0343ba8771398cca967fed +msgid "" +"`cwltool` supports running containers with Docker, Podman, udocker, and " +"Singularity. You can also use alternative container registries for pulling " +"images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 22ed0b55de38408393af4a8309a995ea +msgid "" +"The [Implementations](basic-concepts.md#implementations) topic in the next " +"section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 5ded73cae5db40ad840c3022e7cd447f +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 23e5613df7c94e5f938c85b14f5441e4 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 3b425afc63d841d4be57c92b25b4ed2d +msgid "" +"This section will show you a brief overview of what CWL is, and where you " +"can learn more about it. No previous knowledge of CWL is required, but you " +"must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 75a26c48d3e04e24abb96d81cb31c94e +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 88b4ecd45ea44dd4befe3ce89b30f6c2 +msgid "" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The " +"example below shows a simple CWL “Hello World” workflow annotated with " +"comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 e1789ef78bd64332a18d8601094a0f72 +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 196ceef96c27434eb4b0b7222c2fe73c +msgid "" +"The example above is just a wrapper for the `echo` command-line tool. " +"Running the workflow above with the default input values will produce the " +"same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 e6a44130c6b44d5bb6451a147f28dd8c +msgid "" +"In CWL, there is a distinction between a command-line tool and a workflow. " +"But for the sake of simplicity, we are using the term “workflow” here. You " +"will learn more about this in the [basic concepts](basic-concepts.md) " +"section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 340b46acc7a34b7b978f5a734f529553 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 139e48dcf0474fea932ca07a0001d208 +msgid "" +"`cwltool` is an implementation of the CWL specification. It is also the CWL " +"*Reference Runner* for the specification, and it is compliant with the " +"latest version of the specification: {{ cwl_version }}. You can install " +"`cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 d6f6e061c0f4434eb6d70f9d84759042 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 cb2b548489df45ee9d49b36116440eea +msgid "" +"If installing the cwltool using the pip command doesn't work for you, the " +"[prerequisites](prerequisites.md) section contains other ways to install " +"`cwltool` and a more detailed list of software and libraries used for " +"following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 aa751bda67ec44ba988642b061e2a094 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 a7e0209af0544b0ab31012864a43886c +msgid "" +"The usage of the `cwltool` command-line executable is basically `cwltool " +"[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " +"workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 d0f424f0041c4635a0559fa32a76c86f +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 eeee96c4e59447aea6b239c63e4bb3e5 +msgid "" +"Or you can override the default value of the input parameter `message`, " +"similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 961a385b340141e980aa4f8791fa2f12 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 c48cd1be543d4ccbab964b28c2e08584 +msgid "" +"Another way of passing values to your workflow input parameters is via an " +"*Inputs Object*. This is a file containing the input fields with their " +"corresponding values. The Inputs Objects file can be written in JSON or " +"YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 e5619164bdf242f0b09cac668adc0ef7 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 9f80772a53154bbeb27895d35435de10 +msgid "" +"You can use this Inputs Object file now to execute the “Hello World” " +"workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 98b6d400cb274d08ad6489adbef08c4b +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 4faabaab56f1444da290cf64cc389f37 +msgid "" +"We used a similar file name for the workflow and for the Inputs Object " +"files. The *-job.json* suffix is very common in Inputs Object files, but it " +"is not a requirement. You can choose any name for your workflows and Inputs " +"Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 48beaccb16a24427bd015c63f9e06d37 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 68035ead1c6844128011ca32c04fd20f +msgid "" +"[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 8fc1ebf21a6f4894a4acfba74a80602b +msgid "" +"The [`common-workflow-language` organization](https://github.com/common-" +"workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 27fbad579d8b4ebeacc6fd3ef7e85a39 +msgid "" +"[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" +"Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 a8791b670848474da292a467f01f8c45 +msgid "" +"[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." +"org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 fc20fa4c04104417b541a67ada2ab9a9 +msgid "" +"The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." +"replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 a93a7797a12b48dfa5bc3a7c50ab88e7 +msgid "" +"[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" +"Workflow_management_system)." +msgstr "" + +#: ../../src/setup.md:9 6f02fa47aca14c59a35b3ab750f5f236 +msgid "" +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. The information on this page has been migrated to the [FAQ](/faq." +"md) section of the new user guide." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 3821c2d16b254672a494522e47386cb0 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: 412a05f3492349a7bd26ea0c30e9bd80 +msgid "" +"Sometimes tools require additional command line options that don't " +"correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: 1232f6c81da141cb8482294eee5955dc +msgid "" +"In this example, we will wrap the Java compiler to compile a java source " +"file to a class file. By default, \"javac\" will create the class files in " +"the same directory as the source file. However, CWL input files (and the " +"directories in which they appear) may be read-only, so we need to instruct " +"\"javac\" to write the class file to the designated output directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: 485bb71673144e3f90f05b420b7079ac +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 0beb10c3133643f6b62c7d4aeec33709 +#: 5d48d9a2e977431f9a3625abaa466f5f +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: fcc1151a2e8b4a84b8595c7f913781a1 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 4a291c7ac7c84257b7402567d8364a36 +msgid "" +"And now invoke `cwltool` providing the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 3b1ae26038fd498ca0ae23aa70a35d3f +msgid "" +"Here we use the `arguments` field to add an additional argument to the " +"command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: 40388ebefb6947089c4a0f6d5d6e92e8 +msgid "" +"This example references a runtime parameter. Runtime parameters provide " +"information about the hardware or software environment when the tool is " +"actually executed. The `$(runtime.outdir)` parameter is the path to the " +"designated output directory. Other parameters include `$(runtime.tmpdir)`, " +"`$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and " +"`$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of " +"the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 a417fdd330db47a3aac07f7006c83ca9 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 99bad0fd9bee428a8d936d5a8e84d97d +msgid "" +"The following are a set of recommended good practices to keep in mind when " +"writing a Common Workflow Language description for a tool or workflow. These " +"guidelines are presented for consideration on a scale of usefulness: " +"although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 935500b0e6e249eba585644cddbd0253 +msgid "" +"No `type: string` parameters for names of input or reference files/" +"directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 96f924d6e02f4005b35d463e49be2982 +msgid "" +"A CWL document (in conjunction with any external components like " +"`Dockerfile`s) is software code. Workflow developers should be aware that " +"the usual rules of software licensing apply to this document. For example, " +"if the workflow is shared publicly, licensing terms must be clear so that a " +"future user understands under what conditions they can run the workflow, " +"modify it and/or combine it with other workflows. For this reason, please " +"consider including a license field in the document. The authors of this " +"guide urge you to choose a pre-existing license rather than trying to write " +"your own (see the link below to learn more about choosing a license), and " +"our recommended practice is to choose a license that allows for re-use by " +"anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 25e0a5c93ccc49bc8b6206c7c2e3de5c +msgid "" +"If possible, the license should be specified with its corresponding [SPDX " +"identifier][spdx]. Construct the metadata field for the license by providing " +"a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is " +"taken from the list of identifiers linked above. See the example snippet " +"below for guidance. For non-standard licenses without an SPDX identifier, " +"provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 34ad53bc5a40446daa0dac4571600d1e +msgid "" +"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" +"Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 4c397ffd2e9148e39bdd614683a98a78 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 1ed7f7e73afb4bd2ad2e29b65d020ff1 +msgid "" +"For more examples of providing metadata within CWL descriptions, see [the " +"Metadata and Authorship section of this User Guide](../topics/metadata-and-" +"authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 13b058dfa3cd4bbea54ae7d5a56c4c50 +msgid "" +"Include [attribution information][license-example] for the author(s) of the " +"CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" +"[orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 69369b917c1a45199343266650b1b220 +msgid "" +"In tool descriptions, list dependencies using short name(s) under " +"`SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 0245a61fd2ef4fb69cbb8d732086fb8f +msgid "" +"Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" +"identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 e9a56e3634a042279cae1745b7820658 +msgid "" +"All `input` and `output` identifiers should reflect their conceptual " +"identity. Use informative names like `unaligned_sequences`, " +"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " +"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 8a180861a66c4aaa9e8fdefd929ed829 +msgid "" +"In tool descriptions, include a list of version(s) of the tool that are " +"known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 00f333a383b64578b32c687b42924a77 +msgid "" +"`format` should be specified for all input and output `File`s. " +"Bioinformatics tools should use format identifiers from [EDAM][edam-" +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with " +"`$namespaces: { iana: \"https://www.iana.org/assignments/media-types/\" }`. " +"[Full IANA media type list][iana-types] (also known as MIME types). For non-" +"bioinformatics tools, use or build an appropriate ontology/controlled " +"vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 6b960d362bb540299f0560c14c5f2d8c +msgid "" +"Mark all input and output `File`s that are read from or written to in a " +"streaming compatible way (only once, no random-access), as `streamable: " +"true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 9cf9342bf0864e87b495913d8e06d021 +msgid "" +"Each `CommandLineTool` description should focus on a single operation only, " +"even if the (sub)command is capable of more. Don't overcomplicate your tool " +"descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 587b048324e447cb85844d8c64ae9a1e +msgid "" +"Custom types should be defined with one external YAML per type definition " +"for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 d8df6bbd5d324f7c9f48edb33e113b75 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 2235174088ad48a89d4fc21223e627b7 +msgid "" +"If useful, include a top-level `doc` as well. This should provide a longer, " +"more detailed description than was provided in the top-level `label` (see " +"above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 a0f0953a1a9f40cebd4dbe028784ff96 +msgid "" +"Use `type: enum` instead of `type: string` for elements with a fixed list of " +"valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 0ec380c683534892b6b8b8fcea84f765 +msgid "" +"Evaluate all use of JavaScript for possible elimination or replacement. One " +"common example: manipulating `File` names and paths? Consider whether one of " +"the [built in `File` properties][file-prop] like `basename`, `nameroot`, " +"`nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 65f23741db4e4a6abda8e5f7e036753a +msgid "" +"Give the tool description to a colleague (preferably at a different " +"institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 34c2caee8eb84e01a37033b67eb4aaba +msgid "" +"Complex workflows with individual components which can be abstracted should " +"utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " +"workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 d7c7484b2f1048aea9802400410f0858 +msgid "" +"Software containers should be made to be conformant to the " +"[\"Recommendations for the packaging and containerizing of bioinformatics " +"software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 a905abc2eead4dbaa035235936025499 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 eb91b6dab34d4d5f9854ac580a6cbde2 +msgid "" +"A command-line tool is a type of Process object that can be run by itself or " +"as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " +"etc. The command-line tool is defined in the `baseCommand` attribute of the " +"command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 7caeb91564634091a932f1270c4f5ef9 +msgid "" +"A CWL command-line tool must also have `inputs` and `outputs`. The following " +"example contains a minimal example of a CWL command-line tool for the `echo` " +"Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 c6ac4a60d102407991f40b892fb60560 +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 51d3ce421db345f5ab19e02fbbc51df2 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 8311d1430e624435b7b04bf2574a90c5 +msgid "" +"The example above uses a simplified form to define inputs and outputs. You " +"will learn more about in the [Inputs](../topics/inputs.md) and in the " +"[Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 d1c03e5f19d64ea89276d126de6e4bda +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 8494b43e98dd424db7d57aa1d731f7b4 +msgid "" +"This indicates whether a process requires outgoing IPv4/IPv6 network access. " +"If a command-line tool is written manually in CWL v1.1+, there is a need to " +"specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 8c4573fb120149269a0fe3a1ba6c9ef8 +msgid "" +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " +"Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: e1c709ac0fb249928d14aeced6551ae0 +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: c26c9c640e0747c8b2c2977c860c9d82 +msgid "" +"Sometimes you need to create a file on the fly from input parameters, such " +"as tools that expect to read their input configuration from a file rather " +"than the command line parameters, or need a small wrapper shell script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: edbe918d7df14cafb440e171e46c6de3 +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: 6d457d9b4ae746d384e65d9a37ca3591 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: 868394c1b8374ee6bbd43463e73d7edc +msgid "" +"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " +"expanded by the CWL engine before creating the file. Here, insert the value " +"at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 08a9e08cba674db09c9bfbef37e9579f +msgid "" +"The _CWL expressions_ are independent of any _shell variables_ used later " +"during command line tool invocation. That means that any genuine need for " +"the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` " +"above is expanded to `${PREFIX}` in the generated file to be evaluated by " +"the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 6f6f437753dd4eddae0b2ea62046fe39 +msgid "" +"To test the above CWL tool, use this job to provide the input value " +"`message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 +#: 096b17907bc3452d9927ef2fb6f5c11f 78ed5d8fb9bd4e068023d2c717e20f62 +#: c3a2e9e6b4414597a17db6d55d98e9d1 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: ac783e6415a44cb59d4b425bac5087b7 +msgid "" +"Before we run this, let us look at each step in a little more detail. The " +"base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: b9e6e15b541149c6a2d3922c11405267 +msgid "" +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML " +"array, we need a `-` on the first line of each element of the array, in this " +"case we have just one element. `entryname:` can have any value, but it must " +"match what was specified in the `baseCommand`. The final part is `entry:`, " +"this is followed by `|-` which is YAML quoting syntax, and means that you " +"are using a multiline string (without it, we would need to write the whole " +"script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 87088899567a4402aeb34605d3c6b06b +msgid "" +"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " +"formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 +#: 304c1bfe5ecd4d26b5dfaf9ad2e2c7f8 3ef7f0e3099147d78fd2d30bfa73cc6b +#: 4fef79a30282456eb9b5dd34a5eec0b1 afe775762ed348e5982b99bcf1451606 +#: f0689cd0e5b34414b6693331186ee4a3 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on the " +"command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 9f1967411aa7497fa43a4851f0645d6e +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 90bd62e4ef8b41e398a5c9b31f132774 +msgid "" +"Sometimes you may want to write your own custom types for use and reuse in " +"CWL descriptions. Use of such custom types can reduce redundancy between " +"multiple descriptions that all use the same type, and also allow for " +"additional customisation/configuration of a tool/analysis without the need " +"to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 3465527b8ff4407587f7c46fa9fa2a98 +msgid "" +"The example below is a CWL description of the [biom convert format][biom] " +"tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 c0cc869690804ada96a5c1813d17b895 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 01f369931c8142c08fe821a0ca31bf92 +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 0b3ff704cdea44e28aee3c704ca98e27 +msgid "" +"___Note:___ To follow the example below, you need to [download the example " +"input file](https://github.com/common-workflow-language/user_guide/blob/main/" +"src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), " +"*rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 cb456bcae0dd41ffbc514eeea283e130 +msgid "" +"On line 29, in `inputs:table_type`, a list of allowable table options to be " +"used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 c610173365d04c57900b22f4024b47b4 +msgid "" +"The reference to a custom type is a combination of the name of the file in " +"which the object is defined (`biom-convert-table.yaml`) and the name of the " +"object within that file (`table_type`) that defines the custom type. In this " +"case the `symbols` array from the imported `biom-convert-table.yaml` file " +"define the allowable table options. For example, in `custom-types.yml`, we " +"pass `OTU table` as an `input` that tells the tool to create an OTU table in " +"hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 c2b2e18d55c94721812431583cfc4725 +msgid "" +"The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 3e61c3920a7a45db8917c348bd44384d +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 cd87d210b03c4da2a7608b40a6bbcca0 +msgid "" +"In order for the custom type to be used in the CWL description, it must be " +"imported. Imports are described in `requirements:SchemaDefRequirement`, as " +"below in the example `custom-types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 7af9ba3219e44ed49b8da781db5d6fb5 +msgid "" +"Note also that the author of this CWL description has also included " +"`ResourceRequirement`s, specifying the minimum amount of RAM and number of " +"cores required for the tool to run successfully, as well as details of the " +"version of the software that the description was written for and other " +"useful metadata. These features are discussed further in other chapters of " +"this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 eae1994f3a4d481b863b5125c7f4a383 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 8bd8c06d416740b69d126eb9f5f24ad3 +msgid "" +"Tools run in a restricted environment and do not inherit most environment " +"variables from the parent process. You can set environment variables for " +"the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 11c6bffc620b4c789b29ab4034a8bfbd +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 89888b1b994546ce8a93f9630b4bb07e +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 191d3010b9244b39bc3bc50246ac7ad7 +msgid "" +"An expression tool is a type of Process that can be run by itself or as a " +"Workflow step. It executes a pure JavaScript expression. It is meant to be " +"used as a way to isolate complex JavaScript expressions that need to operate " +"on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 3437ed6e184748e4af1ef62f32c8cef1 +msgid "" +"Similar to the command-line tool it requires `inputs` and `outputs`. But " +"instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 c3ae1ef318bb4e0fada76c353dd5f6f1 +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 a7f5e04d242c48a7b3deffb5ff6528be +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 32b6841faed044409bc618cba54a22f0 +msgid "" +"We had to use an `InlineJavascriptRequirement` as our expression contains a " +"JavaScript call in `.toUpperCase()`. This means to tools using the " +"expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 6821ba7a84a44d309d245c429948ad09 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 8167269bc3a64c72bd6c909362350a15 +msgid "" +"If you need to manipulate input parameters, include the requirement " +"`InlineJavascriptRequirement` and then anywhere a parameter reference is " +"legal you can provide a fragment of Javascript that will be evaluated by the " +"CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 c0f75603a6024063a6911f17c70908cc +msgid "" +"JavaScript expressions should only be used when absolutely necessary. When " +"manipulating file names, extensions, paths etc, consider whether one of the " +"[built in `File` properties][file-prop] like `basename`, `nameroot`, " +"`nameext`, etc, could be used instead. See the [list of best practices](best-" +"practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 7faec63b389a4c07b6929b7a78f0cc70 +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 d7dca89942f949d58cb18cb94bb7de72 +msgid "" +"As this tool does not require any `inputs` we can run it with an (almost) " +"empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 1abc1a21c0764415b138099e0e21432b +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 b8b5a50a82e44e49a37c6396f1ff9464 +msgid "" +"`empty.yml` contains a description of an empty JSON object. JSON objects " +"descriptions are contained inside curly brackets `{}`, so an empty object is " +"represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 b38d66c12ab74dfc9395e69d9c04bbf5 +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 8417aa7a9d034361a41def6b71e93413 +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 c1f672b377da4605b9c5098ebb6e1147 +msgid "" +"Note that requirements can be provided with the map syntax, as in the " +"example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 af52f5197e8545d2be22cc0f7f03648c +msgid "" +"Or as an array, with each entry (in this case, only `class: " +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " +"describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 5e12ce15018942bf9010ce6519c17b00 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 e2e9c5f7b681427a9589476649e5a9d8 +msgid "" +"Just like [parameter references](parameter-references.md), you can use " +"JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 8a74763ead0147bbaf3892e552fad546 +msgid "" +"From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 0aab7de8d69f49438d4eeed17316df68 +#: 75f90cb870d14d0dbb4c4ee80d32a65e +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 0b9d8268c177489b86b8eaa638dfa063 +#: 204cd6d8375a4462a8247863a96df906 2b7e56ceb4ad49a8b29a58b10bad7c0a +#: 81f15c64379941d8ac2a681b3879761c f11ae7d801db45989b598864dc6291c9 +#: fc4534b475334f7281d1740c9a78f640 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 70e9085b21f640d6893309a3375c0511 +#: f529003dd7a64bc7be0ccef8dbfa84b3 +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 3fceb522ba6245129b826c342eaf31b4 +#: a5f71add5b8345a4bfa02853ef8a6d35 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 018300196ea24550988a0156894b5e85 +#: 2c799286e8204ed9a83c3fc006988139 +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 25d91d6624bd42e7948e29c684e8e441 +msgid "" +"From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 0944d6525c3c460aa4b5a0e72552ca4d +#: 1187b0d330cb470fbea82a8b8c95aa28 265602307ccd42458ba47ac1b689242c +#: 2febce1b1ad74b18af3a9b3fa137c780 3215ee41f96541cbbda60a1167386c2f +#: 80efeab6ec0e447bbe158cbaa57f83d8 8d2bbd91b4ab4faa923fc1a14ec49dd5 +#: b4a6e640275b4fc7a18e3083e86b72a1 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 480b2e4207574b27b8d33dfe5e9ab64e +#: 4b4149a3b97a4de5b2d7fd84bd547ffe 7af1a82df41e40d0a430babafe1bc5e2 +#: be01787b66e34074af32bb45dcce8657 be099ab533504a7596fd56ec1ce7ca5d +#: c8b96271665444608f601a460dd28fb3 cb6dfa7bc68b41929a5247d929c2f94a +#: f7f452e92f6d4a14ba3912c62699019a +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 4811c1b9867b44caa70dec4b91970484 +msgid "" +"From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 0b1f2a8986e0419a90e484d3a945a037 +msgid "" +"From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 dbc02876870d49d2b9e39db4133a0f62 +msgid "" +"From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 97339a3fa43849f7b292f4643b5fe35c +#: da8b81b1e1884406a188fb04825ef90e +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 077e7b0d2dde443699050af8c63ab912 +#: c8cbe3dfd0984221ae72012ea26edc6f +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 3f07f4a8594640c2b2da4da521872b59 +#: 573f7e4b72ec4c47ab2e54e2c4877d9c +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 f03011b3479b47c690604c508d95c263 +msgid "" +"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" +"v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 1ec3f913909b4e04bb602767d23bd85d +#: 2f7130500b8c450fa4af226b18e38407 +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 a5849a856a374cda807ecf48034af915 +msgid "" +"From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 bd8bbd60aaff4e7aacec91bcbad500f4 +#: f0c99004211e4adf8c0b524d5bbcc12b +msgid "" +"From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." +"html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 96c544cf213245cfb3d1f5196223c6cc +#: c6a04d4f3ef24104b0a86f9093935c13 +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 946e0437a48b4d5da2a29d489250cbaa +msgid "" +"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](https://www." +"commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 1f287ebf87ae4e93bd1ac65cc1d01bf4 +msgid "" +"From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 0d0f4f0e12174d588c131afef70efc5f +#: a74e0e3499d644b4a9d999d3555f03de +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 b2e31c38f7cb4ecabd6b9b89ef051c0e +#: ddc9d9ae72a64a76a2a8e2bba22584ee +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 12f86817dfc14f2bb39509886d56017f +#: 8a94f2c3b1674162a268f67935a3025b +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 a800acfefb3f433fae2cdda9ac4a795a +#: bcb58fc2447a4472b86913871b8c12ee +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 5be337d412ba4d48877e991d535e810c +#: e6cf2f8498db4f549193be20d87e16f9 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 3bc61c8197664f12a98d1ac38b421b38 +#: 9973a87f747445ad89ce959420cac5fd +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 0f5dc4f5a4c64f818e2e22f20472ae84 +#: 2ec9d1f191f44686b1cb8622336d6b92 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 5382ff97ad2f419dbe1bed266997aa84 74406f77013443f28d4d6306c54b0df1 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 f594a20dc038457e815dc17bae6e031d +msgid "" +"From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 5814f96ee4ec4822aecad33c8eda0473 c46c44268b2a4b96b1df13e53e82e54c +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 b9824103ef8745bab30b65887c82f62f +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: 28b23f84c64549e7a0fe444ccc3e1b05 fdd5d742a6764e5db2281ed844bf3475 +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: b6123c911c804f3c8cb596d2aa495b2b d81a7d8b7db444409b286e5f1d863968 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: eb6255a0f8d748588d87e7ad38e507bd fffc5a80bd68495396d32b7a1821eb4e +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 b00a8a2a572742e0929470550433e929 +msgid "" +"From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 9b34c95e483e47f3828e79bf929a23b4 c968eebaf0114b23b789e9ce68e7588d +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 7c8fb996d1af4cfdb0d49d8ed2696745 +msgid "" +"Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 75a29e9ff2cf4b5bb6afa87a741a111b +msgid "" +"The requirement `InlineJavascriptRequirement` supports an `expressionLib` " +"attribute that allows users to load external JavaScript files, or to provide " +"inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 5233d8baa8b74391bf8fee5ae2324234 +msgid "" +"Entries added to the `expressionLib` attribute are parsed with the " +"JavaScript engine of a CWL runner. This can be used to include external " +"files or to create JavaScript functions that can be called in other parts of " +"the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 343e8b78a1f94b8cbafac05212e5a333 +msgid "" +"The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl." +"org/v1.0/CommandLineTool.html#Expressions) that the only version of " +"JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-" +"international.org/5.1/). This means that any code that you include or write " +"in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 0657ee8f03d8462ca6ca6fc538386b0d +msgid "" +"For example, we can use `InlineJavascriptRequirement` and write a JavaScript " +"function inline in `expressionLib`. That function can then be used in other " +"parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 e3c593cf50da426f8d9df215c7db0bc9 +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 b971e53c3ed847f1b7c7a6d50e344baf +msgid "" +"Running this CWL workflow will invoke the JavaScript function and result in " +"the `echo` command printing the input message with capital initial letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 d2315d46369f4e9d9c871d7f88f7006e +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 04fdaa45a7ed47d5830181611bda924e +msgid "" +"Let's move the `capitalizeWords` function to an external file, `custom-" +"functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 8d7686f62f314d98aae8c262befd5283 +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 e68ee17607be4a06a66f9fc67624aff5 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 76b85d3729274fc08adfadcbf1172650 +msgid "" +"The `custom-functions.js` file is included in the CWL document with the " +"`$include: custom-functions.js` statement. That makes the functions and " +"variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 29f334957fa940c289f385160cca6d63 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 6d255ae6b92a48fa9b7b98443cc2f5bb +msgid "" +"Finally, note that you can have both inline and external JavaScript code in " +"your CWL document. In this final example we have added another entry to the " +"`expressionLib` attribute with the new function `createHelloWorldMessage`, " +"that calls the `capitalizeWords` function from the external file `custom-" +"functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 89734e7855654b2e8bfddeea96241539 +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 1915f8e68f624027827d28f8e17d2dec +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 750f94edb4f84e45a276f6ab28fad95e +msgid "" +"The `$include` statement can be used to include a file from the local disk " +"or from a remote location. It works with both relative and absolute paths. " +"Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad." +"html#Include) from the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 2e9e8cfaf48a43a88c31a855dac4f748 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 c574b54d998243f28d2caa91434968a7 +msgid "" +"Tools and workflows can take `File` types as input and produce them as " +"output. We also recommend indicating the format for `File` types. This helps " +"document for others how to use your tool while allowing you to do some " +"simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 b0ec34507eea473c91d6ada09a1c5c09 +msgid "" +"For file formats, we recommend referencing existing ontologies (like EDAM in " +"our example), reference a local ontology for your institution, or do not add " +"a file format initially for quick development before sharing your tool with " +"others. You can browse existing [IANA file format listings][IANA] and [EDAM " +"file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 a688e39859734a518c0fcc19f532a432 +msgid "" +"In the next tutorial, we explain the `$namespaces` and `$schemas` section " +"of the document in greater detail, so don't worry about these for now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 e068422ad9b84ca1b27008127928cc0f +msgid "" +"Note that for added value `cwltool` can do some basic reasoning based on " +"file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 8c3ef5e145b14299bf3671add0da56ac +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: 0d92f1c0f1ce448fb698e9b390b45c15 fc4773204ebc4e3789bb076dff0d0393 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 900abc5aa6a940f48f9c93e79cd1c47f +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 0390555b96c84aadbd9325c152972087 +msgid "" +"Below is an example of a parameter file for the example above. We encourage " +"checking in working examples of parameter files for your tool. This allows " +"others to quickly work with your tool, starting from a \"known good\" " +"parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 d5752ee5437b496ca10f4f12b76fc5dc +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 91dc76bb4565473ab948eecf628a405c +msgid "" +"___Note:___ To follow the example below, you need to download the example " +"input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 0b8b9b7f533543a49f876421ce6057d9 +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 1b6cfac3a92347d4b98bb54de1e26870 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 53dd5f476f064cbf9b9826d1e80eb830 +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 420b33d143fc44d1b237bc678f0af663 +msgid "" +"The `inputs` of a tool is a list of input parameters that control how to run " +"the tool. Each parameter has an `id` for the name of parameter, and `type` " +"describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 55136332e3bb48f892cf6a74c67a4ac6 +msgid "" +"Available primitive types are *string*, *int*, *long*, *float*, *double*, " +"and *null*; complex types are *array* and *record*; in addition there are " +"special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 cb2527899cc04b6d8060c4d57883beb5 +msgid "" +"The following example demonstrates some input parameters with different " +"types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 c79668b856b14243b4fad0f46dc5d6d7 +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 ed6f3e5c7b3f403a9a94359983107645 +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 034075eb09db4897a96d3332408427db +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 08181d391cc543a5a81d3257654df213 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 15215522e38242c4b17ec3aa089269d4 +msgid "" +"You can use `cwltool` to create a template input object. That saves you from " +"having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 64bd3382ec234ec8a50217b794b96916 +msgid "" +"You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " +"> inp-job.yml`, and then modify the default values with your desired input " +"values." +msgstr "" + +#: ../../src/topics/inputs.md:44 3611c1ca498a4197a4a6612c60f5f565 +msgid "" +"Notice that \"example_file\", as a `File` type, must be provided as an " +"object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 da924e8142d34e86bcb5de1cd1da71ca +msgid "" +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " +"command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 13c97256a5ee49c99f4010edf9dbc9bf +msgid "" +"Now invoke `cwltool` with the tool description and the input object on the " +"command line, using the command `cwltool inp.cwl inp-job.yml`. The following " +"boxed text describes these two commands and the expected output from the " +"command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 dcc3f2a47a6449efb857af63ed4b65d0 +msgid "" +"The CWL reference runner (cwltool) and other runners create temporary " +"directories with symbolic (\"soft\") links to your input files to ensure " +"that the tools aren't accidentally accessing files that were not explicitly " +"specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 cf54a30ae24f4013bb19f379a7ca67be +msgid "" +"The field `inputBinding` is optional and indicates whether and how the input " +"parameter should appear on the tool's command line. If `inputBinding` is " +"missing, the parameter does not appear on the command line. Let's look at " +"each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 ff75644bae9c46af8379d78360d4c696 +msgid "" +"Boolean types are treated as a flag. If the input parameter " +"\"example_flag\" is \"true\", then `prefix` will be added to the command " +"line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 e90abe59a84e48d4b8d6caa737e087aa +msgid "" +"String types appear on the command line as literal values. The `prefix` is " +"optional, if provided, it appears as a separate argument on the command line " +"before the parameter . In the example above, this is rendered as `--example-" +"string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 9275236d87b646cab1058dd750e11a50 +msgid "" +"Integer (and floating point) types appear on the command line with decimal " +"text representation. When the option `separate` is false (the default value " +"is true), the prefix and value are combined into a single argument. In the " +"example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 6a39929af73f4ba9b6455ed9fd287e08 +msgid "" +"File types appear on the command line as the path to the file. When the " +"parameter type ends with a question mark `?` it indicates that the parameter " +"is optional. In the example above, this is rendered as `--file=/tmp/random/" +"path/whale.txt`. However, if the \"example_file\" parameter were not " +"provided in the input, nothing would appear on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 44ce716561cc4dff8fef1ca59f816c7c +msgid "" +"Input files are read-only. If you wish to update an input file, you must " +"[first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 9f1da592350f40ee88920465e2004148 +msgid "" +"The value of `position` is used to determine where parameter should appear " +"on the command line. Positions are relative to one another, not absolute. " +"As a result, positions do not have to be sequential, three parameters with " +"positions 1, 3, 5 will result in the same command line as 1, 2, 3. More " +"than one parameter can have the same position (ties are broken using the " +"parameter name), and the position field itself is optional. The default " +"position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 5116d91f247f44518eb21840415f6eaa +msgid "" +"The `baseCommand` field will always appear in the final command line before " +"the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 08b26d1688e3470288e73d587f052d88 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 f91994a4279a41bda3de41fe79008c62 +msgid "" +"It is easy to add arrays of input parameters represented to the command " +"line. There are two ways to specify an array parameter. First is to provide " +"`type` field with `type: array` and `items` defining the valid data types " +"that may appear in the array. Alternatively, brackets `[]` may be added " +"after the type name to indicate that input parameter is array of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 4b93a4f980634e88a8f34a38703fc906 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 de3e760ebb0e4ae099deddb978046a2c +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 06ec811e8f0e43b8b929198533ac8082 +#: 797c06f0605d4e4ba306c2803a7834f9 d76d42c490a24b6daed944f45fe7a351 +msgid "" +"Now invoke `cwltool` providing the tool description and the input object on " +"the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 49406f30f62346968bb1250efc940f70 +msgid "" +"The `inputBinding` can appear either on the outer array parameter definition " +"or the inner array element definition, and these produce different behavior " +"when constructing the command line, as shown above. In addition, the " +"`itemSeparator` field, if provided, specifies that array values should be " +"concatenated into a single argument separated by the item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 3d8711f0135e4ab1b59fce94c83b97c0 +msgid "" +"Note that the arrays of inputs are specified inside square brackets `[]` in " +"`array-inputs-job.yml`. Arrays can also be expressed over multiple lines, " +"where array values that are not defined with an associated key are marked by " +"a leading `-`. This will be demonstrated in the next lesson and is discussed " +"in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify " +"arrays of arrays, arrays of records, and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 6f146779d6a84888948751b8b1fd0515 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 e5970a83876e4b5e9a02f2ab0030eb83 +msgid "" +"Sometimes an underlying tool has several arguments that must be provided " +"together (they are dependent) or several arguments that cannot be provided " +"together (they are exclusive). You can use records and type unions to group " +"parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 0db71b22173846d7b8d4aeb66d2ed8ed +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 f90fd48656a7424aac304987adf1b068 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 3c8bd9134a1c4bda9461362df3257d6b +msgid "" +"In the first example, you can't provide `itemA` without also providing " +"`itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 63bd06780bb949e5b1a1d10389c8c23f +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 0d448baa57f14e7783d3167611e8c659 +msgid "" +"In the second example, `itemC` and `itemD` are exclusive, so only the first " +"matching item (`itemC`) is added to the command line and remaining item " +"(`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 202239a6e90044e39b676d641aa6d58a +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 512ecb3349b0450cb741de4ed2d2e850 +msgid "" +"In the third example, only `itemD` is provided, so it appears on the command " +"line." +msgstr "" + +#: ../../src/topics/inputs.md:255 185ff0bb49e841c592b29112eb171bdc +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 6cd5df09e4594d78a526f199ac577881 +msgid "" +"If you use exclusive input parameters combined with expressions, you need to " +"be aware that the `inputs` JavaScript object will contain one of the " +"exclusive input values. This means that you might need to use an **or** " +"boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 9db9f784a5cd4ca5b90691d1e2e827ea +msgid "" +"Let's use an example that contains an exclusive `file_format` input " +"parameter that accepts `null` (i.e. no value provided), or any value from an " +"enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 09b1db3cc6c845058cf0ad4c24d71733 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 84aa6e0c479f4528836691005129056e +msgid "" +"Note how the JavaScript expression uses the value of the exclusive input " +"parameter without taking into consideration a `null` value. If you provide a " +"valid value, such as “fasta” (one of the values of the enum), your command " +"should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 76611ebb19764bdc8a1f6eacfb76138f +msgid "" +"However, if you do not provide any input value, then `file_format` will be " +"evaluated to a `null` value, which does not match the expected type for the " +"output field (a `string`), resulting in failure when running your workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 bf9750d215be4294b1cf1e0490a0796a +msgid "" +"To correct it, you must remember to use an or operator in your JavaScript " +"expression when using exclusive parameters, or any parameter that allows " +"`null`. For example, the expression could be changed to `$(inputs." +"file_format || 'auto')`, to have a default value if none was provided in the " +"command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: 612f9efa0ed04559a174c37958def6f7 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: 57eb990c11f044dfb60c012a92a30eb1 +msgid "" +"Implementation extensions not required for correct execution (for example, " +"fields related to GUI presentation) and metadata about the tool or workflow " +"itself (for example, authorship for use in citations) may be provided as " +"additional fields on any object. Such extensions fields (e.g. `format: edam:" +"format_2572`) can use a namespace prefix listed in the `$namespaces` section " +"of the document (e.g. edam: http://edamontology.org/) as described in the " +"[Schema Salad specification][schema-salad]. Once you add the namespace " +"prefix, you can access it anywhere in the document as shown below. " +"Otherwise, one must use full URLs: `format: http://edamontology.org/" +"format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: a6e6155cb8ff40fb9d8b1fff3e94fb02 +msgid "" +"For all developers, we recommend the following minimal metadata for your " +"tool and workflows. This example includes metadata allowing others to cite " +"your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 063c28fc9e654dfd91c66da164ac1d3d +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: 8fcd2ae1ce8d4c7f951281ced81ab32d +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: 639533652456427480fa311da7beb4f0 +msgid "" +"For those that are highly motivated, it is also possible to annotate your " +"tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints at " +"hardware requirements in order to use the tool, and a few more metadata " +"fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 266808daf2004bbd9830045fbc67a541 +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 fd9b715bfa3243b19a919ad19843232d +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 fb568063fa7a4cbe83c271772d3d62bc +msgid "" +"An Operation is a type of CWL process, just like a workflow, a command-line " +"tool, or an expression tool. It is a step of a workflow that specifies " +"inputs and outputs, but it does not provide enough information to be " +"executed." +msgstr "" + +#: ../../src/topics/operations.md:7 981486166754435cbcd8152e93679405 +msgid "" +"You can create operations to visualize a workflow during development, before " +"you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 7b165718ffeb42e793c97fad807f216f +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 5e31cddd14414d31b7bd0a6c2745d272 +msgid "" +"The `uppercase` step of the workflow is an operation. It can be used like a " +"command line tool or an expression. You can also plot it with the CWL Viewer " +"or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 02c372245dc9453ea0841026335e405b +msgid "" +"The output of the command above can be rendered with a Graphviz renderer. " +"The following image is rendered with the Sphinx Graphviz directive (this " +"user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 d331327285d1434e8c17187737345919 +msgid "" +"If you try running it with `cwltool`, the command will fail since `cwltool` " +"does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 72705f8940bb4194bc5554fcc29eed49 +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 76b7c63107e94323859904415d07d31c +msgid "" +"CWL runners may come up with ways to bind operations to concrete steps. A " +"CWL runner could, for instance, use abstract operations with ID's that " +"correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 ebf56d267612461799bf801136e61b69 +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 f9cff6b272a24ef6ada90e263c1b1784 +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 e482821911004cdd8c3ff1539c69368a +msgid "" +"The `outputs` of a tool is a list of output parameters that should be " +"returned after running the tool. Each parameter has an `id` for the name of " +"parameter, and `type` describing what types of values are valid for that " +"parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 e11fcfe1e84b476ea879810b76ff2cb8 +msgid "" +"When a tool runs under CWL, the starting working directory is the designated " +"output directory. The underlying tool or script must record its results in " +"the form of files created in the output directory. The output parameters " +"returned by the CWL tool are either the output files themselves, or come " +"from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 65c73a37f06a4782bf43f4acf4f1c77e +msgid "" +"The following example demonstrates how to return a file that has been " +"extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 e172dde545164fefac826d910ddd399e +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 225f4d04c28149898f06bd771f741358 +msgid "" +"In previous examples, the `baseCommand` was just a string, with any " +"arguments passed as CWL inputs. Instead of a single string we can use an " +"_array of strings_. The first element is the command to run, and any " +"subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 14e9e446768a454ea786b3256b49632e +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 4bd659cee1904868a7c33345f94f1300 +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 8803a28ccff846eea7d06f4bd908c763 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 661b62e554d64e449c69e475e5188f99 +msgid "" +"And now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 44cdca5b777441baa246c87940df7264 +msgid "" +"The field `outputBinding` describes how to set the value of each output " +"parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 edb34af3b22d418d9a6178c0ecbb8b80 +msgid "" +"The `glob` field consists of the name of a file in the output directory. If " +"you don't know name of the file in advance, you can use a wildcard pattern " +"like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 10e68fad866f4187981f0b365b957b03 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 77e1261484964ba9ac67d9fc9139a1d6 +msgid "" +"To capture a tool's standard output stream, add the `stdout` field with the " +"name of the file where the output stream should go. Then add `type: stdout` " +"on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 c66bd08354d54ccb9e3e1da89634a816 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 7d4056355da1451dbed6733fba8c3c38 +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 8fed80f9633a4e87a67c651dc3160ce6 +msgid "" +"You can also capture multiple output files into an array of files using " +"`glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 6cba36e037d54f93add05fb16d2359bd +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 08862892ecf849a1ba2f25ecc9e98227 +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 c5dcc68bb28041b3b96ac1af716b0db8 +msgid "" +"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " +"expected outputs is specified in `array-outputs-job.yml` with each entry " +"marked by a leading `-`. This format can also be used in CWL descriptions to " +"mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 53b95fd10d61462daf153d45e5517dad +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 0702e71de81e493dac08a91d667569e3 +msgid "" +"In a previous example, we extracted a file using the \"tar\" program. " +"However, that example was very limited because it assumed that the file we " +"were interested in was called \"hello.txt\", and this was written into the `." +"cwl` file. This is not the best way to do this, as the \"hello.txt\" " +"filename may vary or be dependent on the input file(s) used. To avoid this " +"we can specify the name of the file we want in the job parameters file (`." +"yml`). In this example, you will see how to reference the value of input " +"parameters dynamically from other fields, which will allow us to then " +"specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 a1703da32ad64fd2b8bdd423605b50bd +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 2f32531e47b4465594d41ddd218fb2fd +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 501dd6f9dbb1438f9a59f6a025639f35 +msgid "" +"Create your input files and invoke `cwltool` with the tool description and " +"the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 1bcdd99111bd4bc5b75a8297bb61d9bb +msgid "" +"Certain fields permit parameter references which are enclosed in `$(...)`. " +"These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 32eae36c593e43a9a6b4e103a0c2028a +msgid "" +"References are written using a subset of Javascript syntax. In this " +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " +"`$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 1d785e8a450140a982142aa0fa906257 +msgid "" +"The value of the \"inputs\" variable is the input object provided when the " +"CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 e862bb8bc3e84e24a2aa5ec34298cfd5 +msgid "" +"Note that because `File` parameters are objects, to get the path to an input " +"file you must reference the path field on a file object; to reference the " +"path to the tar file in the above example you would write `$(inputs.tarfile." +"path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 46ffaab11be040cea96a294d9a814738 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 890d619c415741179c83ffcd56833fbe +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 373e1847d9f745d7a749928642c8e0e3 +msgid "" +"From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 90d3624e062c41c7a6d1a9824515d0df +msgid "" +"From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 76d09490bd464b708c28991dbff0104e +msgid "" +"From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 f33c76e590dd4feaac1e3cf568069d33 +msgid "" +"From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 74ed4a06c1984c58826ddceb1a45a4ea +msgid "" +"From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 eba3362d34354daa89dc516722c6fbd0 +msgid "" +"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" +"v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 e924874af32d4be19c5e8446768226dd +msgid "" +"From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 b162113f364445af9ff1bfc8a6610e13 +msgid "" +"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." +"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 aa721077e16948c3a5bb8ef5bd7aff04 +msgid "" +"From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 2fad0c2bc2834350826b22c454d33cf0 +msgid "" +"From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: 9e303aa89a9b4447b0dbdc5ac0a0eb9e +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: 7a4eb47c25a54d11a00eb73e9333ad1c +msgid "" +"From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: 8a957bc8e577476bb59647661b3c0990 +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: 2b31f1dec3f5498e9e363a4f1f50dc8d +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 5a5f84ecc2f449bf9f037dc9da0ac670 +msgid "" +"Often, tool descriptions will be written for a specific version of a " +"software. To make it easier for others to use your descriptions, you can " +"include a `SoftwareRequirement` field in the `hints` section. This may also " +"help to avoid confusion about which version of a tool the description was " +"written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: ee89f1526c1f4452b4e36ba67bb59747 +msgid "" +"In this example, the software requirement being described is InterProScan " +"version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: c76cec44f5424f6087df28aa33c521a2 +msgid "" +"Depending on your CWL runner, these hints may be used to check that the " +"required software is installed and available before the job is run. To " +"enable these checks with the reference implementation, use the [dependency " +"resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 072d7b3ce3284ed994ff0736b43bbb86 +msgid "" +"As well as a version number, a unique resource identifier (URI) for the tool " +"is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked " +"up in the [SciCrunch][scicrunch] registry, which provides a portal for " +"finding, tracking, and referring to scientific resources consistently. If " +"you want to specify a tool as a `SoftwareRequirement`, search for the tool " +"on SciCrunch and use the RRID that it has been assigned in the registry. " +"(Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool " +"to SciCrunch). You can use this RRID to refer to the tool (via [identifiers." +"org][identifiers]) in the `specs` field of your requirement description. " +"Other good choices, in order of preference, are to include the DOI for the " +"main tool citation and the URL to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 395d611104604a28b78e11b112a95027 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 811b4db0b1794fa89dc870f6cb59a3cd +msgid "" +"Normally, input files are located in a read-only directory separate from the " +"output directory. This causes problems if the underlying tool expects to " +"write its output files alongside the input file in the same directory. You " +"use `InitialWorkDirRequirement` to stage input files into the output " +"directory. In this example, we use a JavaScript expression to extract the " +"base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 7159b5c5023c47128057c4116cce69f4 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 3bfa6791d78f43629de90345f4441ebb +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 9a6bd5b684a740ed9e8993d9f8607774 +msgid "" +"In this section you will find ways to troubleshoot when you have problems " +"executing CWL. We focus on `cwltool` here but some of these techniques may " +"apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 6db8a02139644598894220d538c590b9 +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 f0da0f6283d44bcc95224eb9fe2d1764 +msgid "" +"You can use the `--cachedir` option when running a workflow to tell " +"`cwltool` to cache intermediate files (files that are not input nor output " +"files, but created while your workflow is running). By default, these files " +"are created in a temporary directory but writing them to a separate " +"directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 e2fc28b44ffe4254892a7c7973dc80c4 +msgid "" +"In the following example `troubleshooting-wf1.cwl` we have two steps, " +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | " +"rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW " +"olleH\". However, the second step, `step_b`, **has a typo**, where instead " +"of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 505c7cf9ee9c4af1aeed29002eed1b33 +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 4c31fd11a28943538690d04baa2b5dd0 +msgid "" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " +"(`cwltool` will create the directory for you if it does not exist already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 a8532ac700014db4bd8ef690a27fb844 +msgid "" +"The workflow is in the `permanentFail` status due to `step_b` failing to " +"execute the non-existent `revv` command. The `step_a` was executed " +"successfully and its output has been cached in your `cachedir` location. You " +"can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 94a6148512b24b90b87fd1312a926d75 +msgid "" +"Each workflow step has received a unique ID (the long value that looks like " +"a hash). The `${HASH}.status` files display the status of each step executed " +"by the workflow. And the `step_a` output file `stdout.txt` is visible in the " +"output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 ec4165b7c25c449db6a8804161805e80 +msgid "" +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in " +"the `step_b`). After fixing the typo, when you execute `cwltool` with the " +"same arguments as the previous time, note that now `cwltool` output contains " +"information about pre-cached outputs for `step_a`, and about a new cache " +"entry for the output of `step_b`. Also note that the status of `step_b` is " +"now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 5c0b71a6376848d4aa491854ea2d185d +msgid "" +"In this example the workflow step `step_a` was not re-evaluated as it had " +"been cached, and there was no change in its execution or output. " +"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " +"`step_b` after we fixed the executable name. This technique is useful for " +"troubleshooting your CWL documents and also as a way to prevent `cwltool` to " +"re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 95b832552e8443ea9c652f8c95afc01e +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 561fc9c561bc492ea82c17784dfd439c +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 2420b16855cf4b25af5bcb87413f6dd9 +msgid "" +"[Docker][docker] containers simplify software installation by providing a " +"complete known-good runtime for software and its dependencies. However, " +"containers are also purposefully isolated from the host system, so in order " +"to run a tool inside a Docker container there is additional work to ensure " +"that input files are available inside the container and output files can be " +"recovered from the container. A CWL runner can perform this work " +"automatically, allowing you to use Docker to simplify your software " +"management while avoiding the complexity of invoking and managing Docker " +"containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 f5266ee2c2b34170bc89cb501b869893 +msgid "" +"One of the responsibilities of the CWL runner is to adjust the paths of " +"input files to reflect the location where they appear inside the container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 728166bf41504e1d89b755400742a1b4 +msgid "" +"This example runs a simple Node.js script inside a Docker container which " +"will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 104351ac29d247cb8e017228e2c9b3d8 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 e11a38bfb30b404c99d223647960cb16 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 7ed0bd21e998417cb02fdcb8e44734b6 +msgid "" +"Before we run this, let's just break it down and see what some bits do. " +"Most of this has been explained in previous sections, the only part that is " +"really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 9dcddf6812ba4bc2a7d6c5fcdb978a68 +msgid "" +"`baseCommand: node` tells CWL that we will be running this command using the " +"Node Js runtime that is meant for Javascript files. We then need to specify " +"some `hints` for how to find the container we want. In this case we list " +"just our requirements for the docker container in `DockerRequirements`. The " +"`dockerPull:` parameter takes the same value that you would pass to a " +"`docker pull` command. That is, the name of the container image (you can " +"even specify the tag, which is good idea for best practices when using " +"containers for reproducible research). In this case we have used a container " +"called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 bc1a09475f154562a4db445bf81ac92f +msgid "" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " +"the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 2e117019ace84604a8ed5a31214c2587 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 d0d5b2a1a008411e92859a72101088c1 +msgid "" +"Notice the CWL runner has constructed a Docker command line to run the " +"script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 591d1cd0282b4095a267b44da7d59804 +msgid "" +"In this example, the path to the script `hello.js` is `/home/me/cwl/" +"user_guide/hello.js` outside the container but `/var/lib/cwl/" +"job369354770_examples/hello.js` inside the container, as reflected in the " +"invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 9f989fff165448ecbcaad6adc0f58d6b +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 212c82dca23645e89d8b5bb7599f2d25 +msgid "" +"A workflow is a CWL processing unit that executes command-line tools, " +"expression tools, or workflows (sub-workflows) as steps. It must have " +"`inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 7530029ec04746f2a888dcbc10aa5ce4 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 c1f1d644b37b4f018b87e15249d8758d +msgid "" +"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " +"command-line tool, and the expression tool showed in the earlier examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 2d07232b7d9c415b8ad971e8cbcd9577 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 fa1f770ffeba4b74bcb200cd3949e070 +msgid "" +"A command-line tool or expression tool can also be written directly in the " +"same CWL document as the workflow. For example, we can rewrite the `echo-" +"uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 570020792e824c2ba732bcc2c0134aa1 +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 8a50c511004941d0917a8f0d471467f0 +msgid "" +"Having separate files helps with modularity and code organization. But it " +"can be helpful writing everything in a single file for development. There " +"are other ways to combine multiple files into a single file (e.g. `cwltool --" +"pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 4d2bf0341836405d9729c47d8020faea +msgid "" +"For a sub-workflows you need to enable the requirement " +"`SubworkflowFeatureRequirement`. It is covered in another section of this " +"user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 dd6fc85f74984517b284853a0d46c122 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 f857d80cd5d84622a560c895ab260a92 +msgid "" +"This workflow extracts a java source file from a tar file and then compiles " +"it." +msgstr "" + +#: ../../src/topics/workflows.md:170 02e7e81cdf7e4226973f910cd57b8ccf +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 +#: 3a88d92f41aa4daaad4f4cc6829184b3 646367f222ea41e5987561941d17c4f9 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 aaba75eb272245db82d072fed97b311c +msgid "" +"[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" +"github.com/common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/" +"_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 f8a6e1af5f0349a5a384be0629c37ac8 +msgid "" +"Use a YAML or a JSON object in a separate file to describe the input of a " +"run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 c4f854c7a279404da3688bdf424c7c5e +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 d383ce45139944cb85768627965d9467 +msgid "" +"Next, create a sample Java file and add it to a tar file to use with the " +"command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 84293afa7a6c40f2af0b980c89581fc7 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 e66daf8af53849109936c36ca7d2b2c9 +msgid "" +"The `cwlVersion` field indicates the version of the CWL spec used by the " +"document. The `class` field indicates this document describes a workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 8fbfbb587b264dcf98a3cea16dd36ef3 +msgid "" +"The `inputs` section describes the inputs of the workflow. This is a list " +"of input parameters where each parameter consists of an identifier and a " +"data type. These parameters can be used as sources for input to specific " +"workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 5cdbc4771ea841b4960362b930de2af6 +msgid "" +"The `outputs` section describes the outputs of the workflow. This is a list " +"of output parameters where each parameter consists of an identifier and a " +"data type. The `outputSource` connects the output parameter `classfile` of " +"the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 2e8a41fe43984dc6b4cf430e1ff66b28 +msgid "" +"The `steps` section describes the actual steps of the workflow. In this " +"example, the first step extracts a file from a tar file, and the second step " +"compiles the file from the first step using the java compiler. Workflow " +"steps are not necessarily run in the order they are listed, instead the " +"order is determined by the dependencies between steps (using `source`). In " +"addition, workflow steps which do not depend on one another may run in " +"parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 78c20aa5a5724da6a4c908849c571334 +msgid "" +"The first step, `untar` runs `tar-param.cwl` (described previously in " +"[Parameter References](parameter-references.md)). This tool has two input " +"parameters, `tarfile` and `extractfile` and one output parameter " +"`extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 1606a2f059eb4b0c9e90f2f0cbbe779b +msgid "" +"The ``in`` section of the workflow step connects these two input parameters " +"to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using " +"`source`. This means that when the workflow step is executed, the values " +"assigned to `tarball` and `name_of_file_to_extract` will be used for the " +"parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 b456b11e2760479bbf81a773a3e1f8ee +msgid "" +"The `out` section of the workflow step lists the output parameters that are " +"expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 0fa01fcec32049c989ad1d68841c74de +msgid "" +"The second step `compile` depends on the results from the first step by " +"connecting the input parameter `src` to the output parameter of `untar` " +"using `untar/extracted_file`. It runs `arguments.cwl` (described previously " +"in [Additional Arguments and Parameters](additional-arguments-and-parameters." +"md)). The output of this step `classfile` is connected to the `outputs` " +"section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 2bc9829f95584a269eb577c610b2a80c +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 0e5e6445bfcb42a4bd03612316dd7225 +msgid "" +"Workflows are ways to combine multiple tools to perform a larger operations. " +"We can also think of a workflow as being a tool itself; a CWL workflow can " +"be used as a step in another CWL workflow, if the workflow engine supports " +"the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 0b83c1028b0e43ba972609e4302bc8a2 +msgid "" +"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " +"workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 cbe1ef068b0c417b953655e132333447 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 a691c36a15044b11a6d037d16f818a6d +msgid "" +"This two-step workflow starts with the `create-tar` step which is connected " +"to the `compile` step in orange; `compile` is another workflow, diagrammed " +"on the right. In purple we see the fixed string `\"Hello.java\"` being " +"supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 2e9797fcd4f04f56b5d2b2f1a3e306d5 +msgid "" +"\"Visualization \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 28f4139911b44eeeb7afd31e9f7cae7b +msgid "" +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " +"CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped " +"to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 4a6cb397a20241beab24d956920a8379 +msgid "" +"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " +"running it we had to provide a job file to denote the tar file and `*.java` " +"filename. This is generally best-practice, as it means it can be reused in " +"multiple parent workflows, or even in multiple steps within the same " +"workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 dccb5472a5dc42b7946dd9245a71ecf0 +msgid "" +"Here we use `default:` to hard-code `\"Hello.java\"` as the " +"`name_of_file_to_extract` input, however our workflow also requires a tar " +"file at `tarball`, which we will prepare in the `create-tar` step. At this " +"point it is probably a good idea to refactor `1st-workflow.cwl` to have more " +"specific input/output names, as those also appear in its usage as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 de1e18b69f654cabb75e52b47058030a +msgid "" +"It is also possible to do a less generic approach and avoid external " +"dependencies in the job file. So in this workflow we can generate a hard-" +"coded `Hello.java` file using the previously mentioned " +"`InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 b947e62f4b3b4c10b95737f1839bcc5a +msgid "" +"In this case our step can assume `Hello.java` rather than be parameterized, " +"so we can use hardcoded values `hello.tar` and `Hello.java` in a " +"`baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 2ed0258a3a104ed5ba3b6b95ad998839 +msgid "" +"Did you notice that we didn't split out the `tar --create` tool to a " +"separate file, but rather embedded it within the CWL Workflow file? This is " +"generally not best practice, as the tool then can't be reused. The reason " +"for doing it in this case is because the command line is hard-coded with " +"filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 6584c0995288450b8a01c35fa231afb6 +msgid "" +"In this example we had to prepare a tar file outside, but only because our " +"inner workflow was designed to take that as an input. A better refactoring " +"of the inner workflow would be to take a list of Java files to compile, " +"which would simplify its usage as a tool step in other workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 19237513fd134c33801a7af08f74e70c +msgid "" +"Nested workflows can be a powerful feature to generate higher-level " +"functional and reusable workflow units - but just like for creating a CWL " +"Tool description, care must be taken to improve its usability in multiple " +"workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 b66e0d0a36994b3182a3784bda8ffc19 +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 3bfb9851302248568bb4535ddc87a27f +msgid "" +"Now that we know how to write workflows, we can start utilizing the " +"`ScatterFeatureRequirement`. This feature tells the runner that you wish to " +"run a tool or workflow multiple times over a list of inputs. The workflow " +"then takes the input(s) as an array and will run the specified step(s) on " +"each element of the array as if it were a single input. This allows you to " +"run the same workflow on multiple inputs without having to generate many " +"different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 78a5a600f8cc49ce8055c77a596ad833 +msgid "" +"The most common reason a new user might want to use scatter is to perform " +"the same analysis on different samples. Let's start with a simple workflow " +"that calls our first example (`hello_world.cwl`) and takes an array of " +"strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 f9618882e0a14a0b84ff9751346dc291 +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 4fe03daddd304a9b828fdd1c29f0d072 +msgid "" +"Aside from the `requirements` section including `ScatterFeatureRequirement`, " +"what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 7ab022708a9642ab8aa2e79ea7810381 +msgid "" +"First of all, notice that the main workflow level input here requires an " +"array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 fe144641fc8040b283f15b2b99ecb5a2 +msgid "" +"Here we've added a new field to the step `echo` called `scatter`. This field " +"tells the runner that we'd like to scatter over this input for this " +"particular step. Note that the input name listed after scatter is the one of " +"the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 f13d1b071a7f4a75a4cdee40ecef14fa +msgid "" +"For our first scatter, it's as simple as that! Since our tool doesn't " +"collect any outputs, we still use `outputs: []` in our workflow, but if you " +"expect that the final output of your workflow will now have multiple outputs " +"to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 b0b2e63d2b8a4fd0983e976c16440da4 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 47ac993a90fe46ca92e97d6b67b3276b +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 f5b8681b3c3b4890a86d7b9fb812d958 +msgid "" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " +"calls the command `echo` on a message. If we invoke `cwltool scatter-" +"workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 74e70fec6d2447bbbd2a5bc8af1fa58c +msgid "" +"You can see that the workflow calls echo multiple times on each element of " +"our `message_array`. Ok, so how about if we want to scatter over two steps " +"in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 76fed9e7ad1d4792b7bb364bb684eeb2 +msgid "" +"Let's perform a simple echo like above, but capturing `stdout` by adding the " +"following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 bef387d9be1f4ca19a97023cfdd1c910 +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 eea1be83da574f39914566d835701b4a +msgid "" +"And add a second step that uses `wc` to count the characters in each file. " +"See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 2043f12eb2ce4424b133e0dc0b62aafc +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 87ba95507fc44dbca4cb6c5283ce50f9 +msgid "" +"Now, how do we incorporate scatter? Remember the scatter field is under each " +"step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 e6e1a79638d74547b00c64e3c8b05710 +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 03fb16e74bf14c49b43e35ef6cb45030 +msgid "" +"Here we have placed the scatter field under each step. This is fine for this " +"example since it runs quickly, but if you're running many samples for a more " +"complex workflow, you may wish to consider an alternative. Here we are " +"running scatter on each step independently, but since the second step is not " +"dependent on the first step completing all languages, we aren't using the " +"scatter functionality efficiently. The second step expects an array as input " +"from the first step, so it will wait until everything in step one is " +"finished before doing anything. Pretend that `echo Hello World!` takes 1 " +"minute to perform, `wc -c` on the output takes 3 minutes and that `echo " +"Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 " +"minutes. Even though `echo Hello World!` could finish in 4 minutes, it will " +"actually finish in 8 minutes because the first step must wait on `echo Hallo " +"welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 eca3380c60094df2b91b44b5f7718fae +msgid "" +"Ok, so how do we scatter on steps that can proceed independent of other " +"samples? Remember from [Nested Workflows](#nested-workflows), that we can " +"make an entire workflow a single step in another workflow! Convert our two-" +"step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 6c61733fe4284f51a6b46e89cafe78c4 +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 0585f83162c349969391c9456a884f28 +msgid "" +"Now the scatter acts on a single step, but that step consists of two steps " +"so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 f209343966db4d46b4611d3620c3b496 +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 5a2661ce35dc4d79a15da1e17c0a95ec +msgid "" +"This workflow contains a conditional step and is executed based on the " +"input. This allows workflows to skip additional steps based on input " +"parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 8f7ee09c9d6b491195e2d80315dae398 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 966acff0d3d24104ae9673df8a790fb1 +msgid "" +"The first thing you'll notice is that this workflow is only compatible for " +"version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 d60e1df759654f1b873276cf0296f234 +msgid "" +"The first step of the workflow (step1) contains two input properties and " +"will execute foo.cwl when the conditions are met. The new property `when` is " +"where the condition validation takes place. In this case only when `in1` " +"from the workflow contains a value `< 1` this step will be executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 69aa8d3c9d9a4fe4a62875827648d95f +msgid "" +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " +"will pass the first conditional step and will therefore be executed and is " +"shown in the log by `INFO [step step1] start` whereas the second step is " +"skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 fee34c880e964e08b040adf2d3831803 +msgid "" +"When a value of 3 is given the first conditional step will not be executed " +"but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 cb9e82cf4b484ca7be19612b14fbdf33 +msgid "" +"If no conditions are met for example when using `--val 2` the workflow will " +"raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 8e7c3365f0f94038930f71666f05170f +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 cbe6f35c21044054a010767f2f0cae46 +msgid "" +"[YAML][yaml] is a file format designed to be readable by both computers and " +"humans. This guide introduces the features of YAML that are relevant when " +"writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 2cc21093311548cd837aa7b3f0939093 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 6e7ea76e8aeb477cbb8197efed33e53d +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 482e121a6e74428dbe6ad1f772f14684 +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 179290eee12343dd9aa4d49207cf7c68 +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 7880db40e98e4aaabdc96def3d9f515d +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 75f3b499494b445f9f9a532d178cbc10 +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 2b900b2779c84de5bbd3c933c56e5922 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 189db6d0e54a400eb5615e259354827e +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 e689c0e1dcd645348ceed51e91eb9ad0 +msgid "" +"Fundamentally, a file written in YAML consists of a set of _key-value " +"pairs_. Each pair is written as `key: value`, where whitespace after the `:` " +"is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have special " +"meaning in the CWL specification and underscored key names otherwise. For " +"example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 9532ac8e1dda479e890bf970323a0a32 +msgid "" +"The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " +"and `home` - with their four respective values. Values can be character " +"strings, numeric (integer, floating point, or scientific representation), " +"Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 91a057a7d10f438fad10338dd44c013c +msgid "" +"Values may be wrapped in quotation marks, but be aware that this may change " +"the way that they are interpreted i.e. `\"1234\"` will be treated as a " +"character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a " +"command: in CWL all parts of `baseCommand` must be strings so, if you want " +"to specify a fixed numeric value to a command, make sure that you wrap that " +"numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 d18c1f5ef55d4bb6b8334438fcbc96b8 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 dc6869049fc143b4af91d172a419a125 +msgid "" +"You may use `#` to add comments to your CWL and parameter files. Any " +"characters to the right of ` #` will be ignored by the program interpreting " +"the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 c3c7f5ecfedb4884ad5e91bb79ba2a7c +msgid "" +"If there is anything on the line before the comment, be sure to add at least " +"one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 84f16419237a4789ac0f3c682b3a11ee +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 269ca8e05ce14e899fc8b2a00b1e458e +msgid "" +"When describing a tool or workflow with CWL, it is usually necessary to " +"construct more complex, nested representations. Referred to as _maps_, these " +"hierarchical structures are described in YAML by providing additional key-" +"value pairs as the value of any key. These pairs (sometimes referred to as " +"\"children\") are written on new lines under the key to which they belong " +"(the \"parent\"), and should be indented with two spaces (⇥tab characters " +"are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 ce790af50da540eb9108ad89eae037cf +msgid "" +"The YAML above illustrates how to build up complex nested object " +"descriptions relatively quickly. The `inputs` map contains a single key, " +"`example_flag`, which itself contains two keys, `type` and `inputBinding`, " +"while one of these children, `inputBinding`, contains a further two key-" +"value pairs (`position` and `prefix`). See the [Arrays](#arrays) section " +"below for more information about providing multiple values/key-value pairs " +"for a single key. For comparison with the example YAML above, here is a " +"graphical representation of the `inputs` object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 c3c9ef616b5d472a894ad6330267bcd2 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 b8a7360f6e0640aa9a2c4907c1ba3fe8 +msgid "" +"In certain circumstances, it is necessary to provide multiple values or " +"objects for a single key. As we've already seen in the [Maps](#maps) section " +"above, more than one key-value pair can be mapped to a single key. However, " +"it is also possible to define multiple values for a key without having to " +"provide a unique key for each value. We can achieve this with an _array_, " +"where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 363da878600a4d229efe0ba79835d73c +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 209dfb0d0a1148ed962dbb33890a3160 +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 cd3a174dae334d0d977a3234e258bd25 +msgid "" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " +"can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 b0f0b10de8f54e1e951e480f696976f1 +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 b5597e8984ad4e0bad33433c1dab89bd +msgid "" +"Native JSON can be useful in indicating where a field is intentionally left " +"empty (such as `[]` for an empty array), as well as where it makes more " +"sense for the values to be located on the same line (For example, when " +"providing option flags and their values in a shell command). However, as the " +"second example above shows, it can severely affect the readability of a YAML " +"file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 5ad7d551d3d347a097508a8488f9d15c +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 58f80e6944f9402a810b9b02ba3ad917 +msgid "" +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " +"while we wrote this guide, though it also covers features that are not valid " +"in CWL." +msgstr "" + +#: ../../src/tutorials.md:1 8fdcc745f4684fa7816c62782507438e +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 3c933ac074ee4d94b7aeacb7abeaf388 +msgid "" +"This is a list of tutorials provided by the CWL community. Use the `Edit " +"this page` link in the menu if you would like to add another tutorial to the " +"list." +msgstr "" + +#: ../../src/tutorials.md:7 1d6cdf13aa834cb4a682553227d9f725 +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 606cc939c5014e2abdab163e4d726f1b +msgid "" +"[Introduction to Workflows with Common Workflow Language: For Contributors.]" +"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 3505468d39c34a20bc55f431a3c697f7 +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 e5731a11b89e492d8d751100a46c5226 +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 cdfeabb88f6245d9a687197d242ed3f9 +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 997679b781a84add9b6d8b1900deec35 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" diff --git a/locales/pt/LC_MESSAGES/sphinx.po b/locales/pt/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..fc56cb08 --- /dev/null +++ b/locales/pt/LC_MESSAGES/sphinx.po @@ -0,0 +1,30 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: 2023-01-26 13:55+0000\n" +"Last-Translator: Michael Crusoe \n" +"Language-Team: Portuguese \n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" +"X-Generator: Weblate 4.16-dev\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 d65b012160e9455eb4d2628279fffc42 +msgid "Main navigation" +msgstr "Navegação principal" + +#: ../../src/_templates/sidebar-nav-bs.html:3 4b3441eb77f448daa60718b7bfa862db +msgid "Section Navigation" +msgstr "Seção Navegação" diff --git a/locales/pt/LC_MESSAGES/user_guide.po b/locales/pt/LC_MESSAGES/user_guide.po new file mode 100644 index 00000000..b49c961f --- /dev/null +++ b/locales/pt/LC_MESSAGES/user_guide.po @@ -0,0 +1,3769 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-27 16:02+0100\n" +"PO-Revision-Date: 2023-01-25 13:37+0000\n" +"Last-Translator: Michael Crusoe \n" +"Language: pt\n" +"Language-Team: Portuguese \n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../LICENSE.md:2 3eb955b4f3dd4c3188924b97ea6ab592 +msgid "Licenses" +msgstr "Licenças" + +#: ../../LICENSE.md:4 bf4480e7fff4460a87e8f43c11599f07 +msgid "Instructional Material" +msgstr "" + +#: ../../LICENSE.md:6 9e9eab12205d4e82b4fedca520370f4c +msgid "" +"All Common Workflow Language project instructional material and changes to " +"the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable summary " +"of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" +"[cc-by-legal]." +msgstr "" +"Todo o material instrucional do projeto Common Workflow Language e " +"alterações na estrutura também são disponibilizados sob a [licença Creative " +"Commons Attribution][cc-by-human]. O seguinte é um resumo legível por " +"humanos de (e não um substituto para) o [texto legal completo da licença CC " +"BY 4.0][cc-by-legal]." + +#: ../../LICENSE.md:12 a8e98ad541c642e58e201afa625ec791 +msgid "You are free:" +msgstr "Você tem o direito de:" + +#: ../../LICENSE.md:14 b4cb4bc4261347fcb0d2c8a93995ab76 +msgid "" +"to **Share**---copy and redistribute the material in any medium or format" +msgstr "" +"**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " +"formato" + +#: ../../LICENSE.md:15 d66dcbf95ccc41aaa53be523487ec913 +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" + +#: ../../LICENSE.md:17 ca1c299a1b834b868bcdd4ca9f244696 +msgid "for any purpose, even commercially." +msgstr "para qualquer fim, mesmo que comercial." + +#: ../../LICENSE.md:19 6133f79f93be4991a6f5290f72d1a63d +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the license " +"terms:" +msgstr "" +"O licenciante não pode revogar estes direitos desde que você respeite os " +"termos da licença:" + +#: ../../LICENSE.md:24 2d6ce81add1043629b676187f890288c +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow Language " +"project, and, where practical, linking to https://www.commonwl.org/ ), " +"provide a [link to the license][cc-by-human], and indicate if changes were " +"made. You may do so in any reasonable manner, but not in any way that " +"suggests the licensor endorses you or your use." +msgstr "" +"Atribuição — Você deve atribuir o devido crédito (mencionando que o seu " +"trabalho deriva de um trabalho que é «Copyright © The Common Workflow " +"Language project», e, quando prático, criar uma ligação para https://www." +"commonwl.org/ ), fornecer um [link para a licença][cc-by-human], e indicar " +"se foram feitas alterações. Você pode fazê-lo de qualquer forma razoável, " +"mas não de uma forma que sugira que o licenciante o apoia ou aprova o seu " +"uso." + +#: ../../LICENSE.md:32 f3f22597b6f845208a0cce3b3b2c8f5d +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything the " +"license permits. With the understanding that:" +msgstr "" +"**Sem restrições adicionais**---Você não pode aplicar termos jurídicos ou " +"medidas de caráter tecnológico que restrinjam legalmente outros de fazerem " +"algo que a licença permita. Com o entendimento de que:" + +#: ../../LICENSE.md:36 3cfedee64d4e46098a159cb2acdba4ef +msgid "" +"You do not have to comply with the license for elements of the material in " +"the public domain or where your use is permitted by an applicable exception " +"or limitation." +msgstr "" +"Não tem de cumprir com os termos da licença relativamente a elementos do " +"material que estejam no domínio público ou cuja utilização seja permitida " +"por uma exceção ou limitação que seja aplicável." + +#: ../../LICENSE.md:39 c836a570faaf449d9716da5f75556627 +msgid "" +"No warranties are given. The license may not give you all of the permissions " +"necessary for your intended use. For example, other rights such as " +"publicity, privacy, or moral rights may limit how you use the material." +msgstr "" +"Não são dadas quaisquer garantias. A licença pode não lhe dar todas as " +"autorizações necessárias para o uso pretendido. Por exemplo, outros " +"direitos, tais como direitos de imagem, de privacidade ou direitos morais, " +"podem limitar o uso do material." + +#: ../../LICENSE.md:44 896f9966e5014e8a88b060be3063fe09 +msgid "Software" +msgstr "Software" + +#: ../../LICENSE.md:46 007f8613dc234c3fa8d5d92b18af0eb1 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the " +"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" +"Salvo indicação em contrário, os programas de exemplo e outro software " +"fornecido pelo projecto Common Workflow Language são disponibilizados sob a " +"[licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." + +#: ../../LICENSE.md:51 227bc635a06f49dbb771fd9b62157d00 +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 +#: 1861131d3df648ae9e74ce1c87f0be7b a2ffa927deb2451d95ec63528e8078dd +#: d6055d3f15604ce6940770c7b561d4c5 +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece of " +"software, tools and workflows described using CWL are portable across a " +"variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/episodes.md:5 ../../src/setup.md:5 +#: 38b062f219b34e08a46bd8f6525353ec 89e7e1dd05474344a1d929cb492e9caf +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 d3357ff3c8874e368aea0d6062ef6190 +msgid "" +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. Please use the new [Table of Contents](index.md#table-of-" +"contents) to browse the User Guide." +msgstr "" + +#: ../../src/faq.md:1 f2c4882e0e164c2b869e3eb969241061 +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 41099ab64e0544d894bd9e3af2718bda +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 bb6aff70534148fa8a4b01140f7be150 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 70ebc653b0d54d60a866edc0dbf56b57 +msgid "" +"This example demonstrates how to change the name of an input file as part of " +"a tool description. This could be useful when you are taking files produced " +"from another step in a workflow, and don't want to work with the default " +"names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 38b687f707d2438b85df08a445ab816f +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 d48422c020004ef084ca11e6229b5450 +msgid "" +"This example demonstrates how to change the name of an output file from the " +"default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 48765409ab9d48ccbcecceb46ddf2e91 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 a59b8acd72124e2c95d1905ae494d928 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 f36088ba90d24f9f9c7c1bd59deb6f49 +msgid "" +"The first method involves adding the folder containing your scripts to the " +"`PATH` environment variable. This allows you to run the shell script " +"directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 45ee965ee4a7494a8354b82208e2ab45 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 734cc1abe1c841ffac8d0895463d91fc +msgid "" +"After that, make the script executable with the command `chmod +x scriptname." +"sh`" +msgstr "" + +#: ../../src/faq.md:97 f01bc8c4d6134f0ea27dc7f5b39def24 +msgid "" +"Finally, modify your `PATH` to add the directory where your script is " +"located. (It is good practice to use `$HOME/bin` for storing your own " +"scripts)." +msgstr "" + +#: ../../src/faq.md:104 dd6fc2a04e3b476892f05bc5b746d0fa +msgid "" +"Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 e309eaad55144052866ce131eb80fd14 +msgid "" +"When you wish to share your work later, you can place your script in a " +"software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 f0d649a60a13404ebecd540789202b87 +msgid "" +"The second method involves including an input of `type: File` in the script " +"itself:" +msgstr "" + +#: ../../src/faq.md:135 e2b782f88d494de398af0c9002a3ccdc +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 b4a033731fcd4322bd2bb71c609a4cb7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 43a64810b12b4c7d82a5803c3b910fe5 +msgid "" +"Currently, `cwltool` can't cope with missing optional inputs if their input " +"binding makes use of `self`. Below is an example workaround for this, " +"pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 60f009e3714c405695da069204b196ea +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 98916ed9355842e49bef073430e10675 +msgid "" +"Below is an example showing how to specify different strings to be added to " +"a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 9b8f2d0b33db4bbc82aaf5836b6f7ed8 +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 a251693354d24bf0bda4938c8890090a +msgid "" +"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" +"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 f46740ac0acb473583facb9f7528d03c +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 7de1f9e3175b4c2ab156192f28fd3535 +msgid "" +"The input must be an array consisting of exactly one entry for each input " +"link. If \"merge_nested\" is specified with a single link, the value from " +"the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 225c6f08068e41f58eb62f99dc06210f +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 4e741f4e3bc74e10bd9568826e81c478 +msgid "" +"Or in other words: if the destination is of type `File[]` (an array of " +"`File`s) and the source is a single `File` then add " +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " +"add `linkMerge: merge_nested` under the appropriate `in` entry of the " +"destination step." +msgstr "" + +#: ../../src/faq.md:229 bfdb011cb81c4ef9b9e56b24f1e9ccd5 +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 09f385e325f942afaa3dd195c16a18d2 +msgid "" +"To make an input parameter optional, add a question mark to the type " +"declaration." +msgstr "" + +#: ../../src/faq.md:247 c5d087082bb2468483e7ccda3ca45a07 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 41e30b0224a0492f9047b4f320f39a23 +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 f06d073014a44f33a60d947a8c5b0e59 +msgid "" +"For command line flags that require a specific input as the argument an enum " +"type can be declared in CWL. **Specifying null here is known as long form " +"style. It does the same thing as the question mark on the other inputs.**" +msgstr "" + +#: ../../src/faq.md:267 2fb74cd1b41e4fdb81a8f9b3b6c84373 +msgid "" +msgstr "" + +#: ../../src/faq.md:268 09e19f34d0fd4e388d4939cbc2be3436 +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 1ecae448dfcf45a4ae0dd39bd011e449 +msgid "" +"For commandline flags that are either **mutually exclusive** or " +"**dependent** a special record type can be defined. You can also specify " +"null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 6df3d4e918cc4bccb823859ce07b197a +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 086db1a093e64caa88d958150accc19c +msgid "" +"To properly set fields in a record input type, you need to pass a dictionary " +"to the input to properly set the parameters. This is done by using inline " +"JavaScript and returning the dictionary with the key of the field you want " +"to set. The source field is set to indicate the input from the workflow to " +"be used as the value." +msgstr "" + +#: ../../src/faq.md:342 da77c818d8694ab99fb2eccf73083047 +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 254259509ed6462d8ebc296b5f811f44 +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 f7a44f76579d4709a61d2d61bc352b76 +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 d67278e99c684f488f1e3418e1c8c207 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 f5e35ee06cd24edf831589ebaa6193d2 +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 2ffb67e547c446499625a8db9a102da6 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 ee653ff9fefe4771b35e2e76199b536a +msgid "" +"For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "" + +#: ../../src/faq.md:371 02b1eb159e934fd692929f7c30319ddd +msgid "" +"If you can not avoid these dangerous characters, then pass `--relax-path-" +"checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 857024702f624885be706c405b7a088e +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 d664e30899bd463bb48d38adec318dd4 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 9f3957bbe205454e8bffc4b5caac5970 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 6ec3bbc6a1ca4e23b47f025f0732e609 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 3e727d79e65e4c6cb157550e80261c53 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 6e0705f4ab4b4e9093794cb4fccb6be9 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 0047d039317349679fb6a66d18ec8487 +msgid "" +"If it is not possible to change the input identifier, then you can use an " +"alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 8c39608ad0494bee9a4a422cbeb34387 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 7dac53bca8c14a3f9af75cb162cba4f9 +msgid "" +"The CWL standards are built around (optional) Docker format containers. The " +"reference runner and several other CWL implementations support running those " +"Docker format containers using the Singularity engine. Directly specifying a " +"Singularity format container is not part of the CWL standards." +msgstr "" + +#: ../../src/faq.md:450 ffcc38ff98324d71bfeb8d66d4901da7 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 0d7bf2cefe4a4e22b186bdf4d0ed793d +msgid "" +"You can use the --js-console option of cwltool, or " +"you can try creating a JavaScript or TypeScript project for your code, and " +"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" +"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + +#: ../../src/index.md:1 1506b4e7ee014a01bfdb067489501a9e +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 0ce058b5210d46a0b78eb78dbca07a9f +msgid "" +"This guide will introduce you to writing workflows using the [Common " +"Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " +"guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 3404c064950d453d8af446e8b6554cb6 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 1e239cad669648e48694eaf91284766a +msgid "" +"If you find that something is missing from this guide, or if you would like " +"to provide other feedback, file an Issue on the [project repository for this " +"guide][repo]. You can also suggest changes directly in a Pull Request by " +"clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 9dba2e06f1be4a50b1fabaaf216d02b4 +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 ba4074bbb69e4096a808001afaf2e0dc +msgid "" +"If you are a beginner user get started with the [Introduction](/introduction/" +"index.md) section. For advanced users the subsections of the [Topics](/" +"topics/index.md) have detailed information about the most common topics for " +"CWL." +msgstr "" + +#: ../../src/index.md:23 ad34a37bf4ec488bb825a34456f4fe8d +msgid "" +"The Table of Contents is displayed at the top menu and also on the left " +"sidebar. It also appears further down this page but with links to " +"subsections. The right sidebar contains links to the sections of each page, " +"and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 2bd8eb5957ed40f4a72a6b7408044c78 +msgid "Table of Contents" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:1 8bb0df5531474301a185f1ba375320df +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 653373e1f11e4f81ad561378854a71fc +msgid "" +"This section describes the basic concepts for users to get started on " +"working with Common Workflow Language (CWL) workflows. Readers are expected " +"to be familiar with workflow managers, YAML, and comfortable with following " +"instructions for the command-line. The other sections of the user guide " +"cover the same concepts, but in more detail. If you are already familiar " +"with CWL or you are looking for more advanced content, you may want to skip " +"this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 7766227bf91b48b2b9752b625e5a9084 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 032d414ac29740aa9041d89d0ebf70e6 +msgid "" +"The CWL specification is a document written and maintained by the CWL " +"community. The specification has different versions. The version covered in " +"this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 74e92eb0a4e64098b5aaf08d043e0641 +msgid "" +"The specification version can have up to three numbers separated by `.`s " +"(dots). The first number is the major release, used for backward-" +"incompatible changes like the removal of deprecated features. The second " +"number is the minor release, used for new features or smaller changes that " +"are backward-compatible. The last number is used for bug fixes, like typos " +"and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 baa40b445f3c409b9a3e10a85fa38bfd +msgid "" +"The model used for the specification version is called Semantic Versioning. " +"See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 648e94a9d368450dbdac706445254c9f +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 e9ae15124dcd408395fc67e16b50696a +msgid "" +"An implementation of the CWL specification is any software written following " +"what is defined in a version of the specification document. However, " +"implementations may not implement every aspect of the specification. CWL " +"implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 b1c864d6775048cab01eb3de641f6475 +msgid "" +"CWL is well suited for describing large-scale workflows in cluster, cloud " +"and high performance computing environments where tasks are scheduled in " +"parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 a05d24121e534d65947eb26e4dada5b7 +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: ace0388fd04845e79d31ec99a48a8a3f +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 70ecd37237e14ae19539f2bf692882ed +msgid "" +"A process is a computing unit that takes inputs and produces outputs. The " +"behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification " +"{{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 38121b4b00324bebb6499184b3dcb5c1 +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: e0c278f52e824673ac708885d985b7d2 +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: 6b4d0f0651cc46f5abf195b281967913 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 88bdc9e046e4487cb0eee3f1d4819e57 +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 12eed3ef7d444585b150bbdab0665bc8 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: dfc85226313d46f9868dc4de53546a69 +msgid "" +"A command-line tool is a wrapper for a command-line utility like `echo`, " +"`ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: f636b10c47734e589291de95443d8115 +msgid "" +"An expression tool is a wrapper for a JavaScript expression. It can be used " +"to simplify workflows and command-line tools, moving common parts of a " +"workflow execution into reusable JavaScript code that takes inputs and " +"produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: bb51025d04444dd5b16000d5d6a3f41a +msgid "" +"Operation is an abstract process that also takes inputs, produces outputs, " +"and can be used in a workflow. But it is a special operation not so commonly " +"used. It is discussed in the [Operations section](../topics/operations.md) " +"of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 93dbaa0aa2c6493ab22a937c6861fac4 +msgid "" +"The workflow is a process that contains steps. Steps can be other workflows " +"(nested workflows), command-line tools, or expression tools. The inputs of a " +"workflow can be passed to any of its steps, while the outputs produced by " +"its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: fcde5ef65ebf45a3b4b67eec993a1729 +msgid "" +"The CWL specification allows for implementations to provide extra " +"functionality and specify prerequisites to workflows through *requirements*. " +"There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: c8ff34ff5d3b4a508e8c291196d08067 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: fe25f15fc11c49ab827b884d081c3df0 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 2b93b6219142431ca748a404a56ced5d +msgid "" +"`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 0094b13b26014ba3be61769b422802f5 +msgid "" +"Some CWL runners may provide requirements that are not in the specification. " +"For example, GPU requirements are supported in `cwltool` through the " +"`cwltool:CUDARequirement` requirement, but it is not part of the " +"{{ cwl_version }} specification and may not be supported by other CWL " +"runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: 576a0778d3dd44f68cb241346f441660 +msgid "" +"Hints are similar to requirements, but while requirements list features that " +"are required, hints list optional features. Requirements are explained in " +"detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: 7d98949fe97744158fad81f41d780de9 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: fc142b791aa1434aa75b0782248de988 +msgid "" +"The FAIR principles have laid a foundation for sharing and publishing " +"digital assets, and in particular, data. The FAIR principles emphasize " +"machine accessibility and that all digital assets should be Findable, " +"Accessible, Interoperable, and Reusable. Workflows encode the methods by " +"which the scientific process is conducted and via which data are created. It " +"is thus important that workflows support the creation of FAIR data and " +"adhere to the FAIR principles. — [FAIR Computational Workflows](https://" +"workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: c3fc91ae3bae4e3db60e8271e95135a2 +msgid "" +"CWL has roots in \"make\" and many similar tools that determine order of " +"execution, based on dependencies between tasks. However, unlike \"make\", " +"CWL tasks are isolated, and you must be explicit about your inputs and " +"outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 8f097ae5ff6a4be0b7428345362dc55e +msgid "" +"The benefit of explicitness and isolation are flexibility, portability, and " +"scalability; tools and workflows described with CWL can transparently " +"leverage technologies such as Docker and be used with CWL implementations " +"from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 60c56fa6a67346d6966f0d841213e11b +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 7377b155e8694798994bbc911a3f3152 +#: 7699685836064bd89db530a9c1918865 7d187a209ebd4e3ba6c6aeb05743041a +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 3fcbf810c86f4cf7b8499de88147aa95 +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: e242228b6b3d440cbca8418050220267 +msgid "" +"The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 6e01963a01cb49e39692455256679bfc +msgid "" +"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: ed81ea2234b041c79449dcd20f886cb6 +msgid "" +"The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: e8e3996f6a894b4f9cc266b46cb8d756 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: 085e4d1a7a9744d2884f3003c64ca174 +msgid "" +"CWL Operations are covered in the [Operations](../topics/operations.md) " +"section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 dcd96950854f47a6ad4169320c1dab34 +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 c4d17eec31874bf1ae9b49d73537d86c +msgid "" +"This section will guide you through a short introduction to CWL, the " +"prerequisites for following this user guide, and some basic concepts that " +"are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 98a8bdfc7c91436d9cb46abbb7c19c57 +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 244a716e267540c782e627adaea3a413 +msgid "" +"The software and configurations listed in this section are prerequisites for " +"following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements focuses " +"on the CWL reference runner, `cwltool`. You can use another CWL-compatible " +"runner or workflow system, but the results and interface may look different " +"(though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 2cdf453d2c8b4e2ea50555ef0b7364e5 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 53643a4f190c412d9552d1908f408318 +msgid "" +"There are many implementations of the CWL standards. Some are complete CWL " +"runners, while others could be plug-ins or extensions to workflow engines. " +"We have a better explanation in the [Implementations](basic-concepts." +"md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 1df6c63de3914af68f758054fe6955f4 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 ceaa3a6bebab45a0907ee0cad01429a2 +msgid "" +"We recommend using an up-to-date operating system. You can choose any of the " +"following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 1506ac904c6345c5806704a0ccf235aa +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 a616213ed24e427bb91ee33cb21ec131 +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 a4e9ae38103843739f13c62befd21f3e +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 2cd231aac42c4a69a925cea369999a8b +msgid "" +"If you are using Windows, you will have to install the [Windows Subsystem " +"for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). " +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool/blob/main/README.rst#ms-windows-users) for details on " +"installing WSL2. Your operating system also needs internet access and a " +"recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 051d7cd7d3a94baa865d180afdd71688 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 1a93aaf5bd5e4862b15e0636b4478640 +msgid "" +"The first thing you will need for running CWL workflows is a CWL runner. " +"`cwltool` is a Python Open Source project maintained by the CWL community. " +"It is also the CWL reference runner, which means it must support everything " +"in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 edd0613118a2493c876652bdcb9e0fbf +msgid "" +"`cwltool` can be installed with `pip`. We recommend using a virtual " +"environment like `venv` or `conda`. The following commands will create and " +"activate a Python virtual environment using the `venv` module, and install " +"`cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 3448d215c2434866b8a4b340872ba81e +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 4c24d05f65794735b816024c78b63f1c +msgid "" +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool#install) for other ways to install `cwltool` with `apt` and " +"`conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 3167f4a2a8394feda1f848334be62022 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 3c4b67d62c9c4d658ccaafcd1977ec08 +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 30792f78348942e0acdde411342e8830 +msgid "" +"The `cwltool` command has an option to validate CWL tool and workflow " +"descriptions. This option will parse the CWL document, look for syntax " +"errors, and verify that the workflow descriptions are compliant with the CWL " +"standards. However, these actions will be performed without running the " +"document. To validate CWL workflows (or even a standalone command line tool " +"description like the above) pass the `--validate` option to the `cwltool` " +"command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 4473e41281fb4e738e4eb26c2d178934 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 548393974d4d4acc91738f9bc13a3a48 +msgid "" +"You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 2ab3963cf9504ec097eda2b14f3448c4 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 690882dcc29c48acbeb215a8be52eb9e +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 6c3ba51b1e9a4add9203d62cec6ebae9 +msgid "" +"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " +"runner. This simply means that the `cwl-runner` alias command can be invoked " +"independently, and is not reliant on a particular CWL runner program name. " +"Users can invoke `cwl-runner` instead of invoking a CWL runner like " +"`cwltool` directly. The `cwl-runner` is installed by a system administrator " +"or user to point to the preferred CWL implementation. This is convenient for " +"environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 b2360ef646854422ad6c0f90fa49306f +msgid "" +"The CWL community publishes a Python package with the name `cwlref-runner` " +"that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 c9fadfa85a2641378e99a462e8e8d940 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 abb8993ede4d4e479d88d2e848546f68 +msgid "" +"Now you can validate and run your workflow with the `cwl-runner` executable, " +"which will invoke `cwltool`. You should have the same results and output as " +"in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 ba0f7606e6174e53a8bf23c1ccd99250 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 dd2e10f43e8f498cb01de5faa4fccb70 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 e500e9c71c7042169c25b31f21a09142 +msgid "" +"Another way to execute `cwl-runner` is by invoking the file directly. For " +"that, the first thing you need to do is copy `true.cwl` workflow into a new " +"file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 d989516c873f4446bba005f42796b8b9 +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 e9d8610478094a98b5b5a0f568a315de +msgid "" +"Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 d6d8131f91b740189e56ab9d90bee55a +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 def7400a00e84070a4bd80c2367d3bde +msgid "" +"And finally, you can execute it directly in the command-line. On execution, " +"the program specified in the shebang (`cwl-runner`) will be used to execute " +"the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 564e7be94d254e52a6c44b234d6ddc63 +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 bb5fe42ddd814ad4ac1071c0b18f24c2 +msgid "" +"The *shebang* is the two-character sequence `#!` at the beginning of a " +"script. When the script is executable, the operating system will execute the " +"script using the executable specified after the shebang. It is considered a " +"good practice to use `/usr/bin/env ` rather than using a hard-" +"coded location, since `/usr/bin/env ` looks for the " +"`` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 53bb712a68cd49fca4db11e9e507c9a4 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 bdcf61cce5294e45a9f964628a8a66bd +msgid "" +"You can use any text editor with CWL, but for syntax highlighting we " +"recommend an editor with YAML support. Popular editors are Visual Studio " +"Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 28d33daee6e246c8a6d1382208e19c39 +msgid "" +"There are extensions for Visual Studio Code and WebStorm that provide " +"integration with CWL, and features such as customized syntax highlighting " +"and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 b071d7c87b7a4817b871085a652cd580 +msgid "" +"Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 97658a1b16874ba8b0bb748242d0da64 +msgid "" +"cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 6198aa6769b74ef0a2a1ba539789f3ee +msgid "" +"The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 0c17235a374e40099be37b9b8ac8f1f0 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 e3690e656b5a4348845c654689935a88 +msgid "" +"`cwltool` uses Docker to run tools, workflows, and workflow steps that " +"specify a software container. Follow the instructions in the Docker " +"documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 2db34e925a81422986ccb868463a7a42 +msgid "" +"You do not need to know how to write and build Docker containers. In the " +"rest of the user guide, we will use existing Docker images for running " +"examples, and to clarify the differences between the execution models with " +"and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 d677fb155b0343ba8771398cca967fed +msgid "" +"`cwltool` supports running containers with Docker, Podman, udocker, and " +"Singularity. You can also use alternative container registries for pulling " +"images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 22ed0b55de38408393af4a8309a995ea +msgid "" +"The [Implementations](basic-concepts.md#implementations) topic in the next " +"section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 5ded73cae5db40ad840c3022e7cd447f +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 23e5613df7c94e5f938c85b14f5441e4 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 3b425afc63d841d4be57c92b25b4ed2d +msgid "" +"This section will show you a brief overview of what CWL is, and where you " +"can learn more about it. No previous knowledge of CWL is required, but you " +"must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 75a26c48d3e04e24abb96d81cb31c94e +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 88b4ecd45ea44dd4befe3ce89b30f6c2 +msgid "" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The " +"example below shows a simple CWL “Hello World” workflow annotated with " +"comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 e1789ef78bd64332a18d8601094a0f72 +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 196ceef96c27434eb4b0b7222c2fe73c +msgid "" +"The example above is just a wrapper for the `echo` command-line tool. " +"Running the workflow above with the default input values will produce the " +"same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 e6a44130c6b44d5bb6451a147f28dd8c +msgid "" +"In CWL, there is a distinction between a command-line tool and a workflow. " +"But for the sake of simplicity, we are using the term “workflow” here. You " +"will learn more about this in the [basic concepts](basic-concepts.md) " +"section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 340b46acc7a34b7b978f5a734f529553 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 139e48dcf0474fea932ca07a0001d208 +msgid "" +"`cwltool` is an implementation of the CWL specification. It is also the CWL " +"*Reference Runner* for the specification, and it is compliant with the " +"latest version of the specification: {{ cwl_version }}. You can install " +"`cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 d6f6e061c0f4434eb6d70f9d84759042 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 cb2b548489df45ee9d49b36116440eea +msgid "" +"If installing the cwltool using the pip command doesn't work for you, the " +"[prerequisites](prerequisites.md) section contains other ways to install " +"`cwltool` and a more detailed list of software and libraries used for " +"following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 aa751bda67ec44ba988642b061e2a094 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 a7e0209af0544b0ab31012864a43886c +msgid "" +"The usage of the `cwltool` command-line executable is basically `cwltool " +"[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " +"workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 d0f424f0041c4635a0559fa32a76c86f +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 eeee96c4e59447aea6b239c63e4bb3e5 +msgid "" +"Or you can override the default value of the input parameter `message`, " +"similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 961a385b340141e980aa4f8791fa2f12 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 c48cd1be543d4ccbab964b28c2e08584 +msgid "" +"Another way of passing values to your workflow input parameters is via an " +"*Inputs Object*. This is a file containing the input fields with their " +"corresponding values. The Inputs Objects file can be written in JSON or " +"YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 e5619164bdf242f0b09cac668adc0ef7 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 9f80772a53154bbeb27895d35435de10 +msgid "" +"You can use this Inputs Object file now to execute the “Hello World” " +"workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 98b6d400cb274d08ad6489adbef08c4b +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 4faabaab56f1444da290cf64cc389f37 +msgid "" +"We used a similar file name for the workflow and for the Inputs Object " +"files. The *-job.json* suffix is very common in Inputs Object files, but it " +"is not a requirement. You can choose any name for your workflows and Inputs " +"Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 48beaccb16a24427bd015c63f9e06d37 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 68035ead1c6844128011ca32c04fd20f +msgid "" +"[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 8fc1ebf21a6f4894a4acfba74a80602b +msgid "" +"The [`common-workflow-language` organization](https://github.com/common-" +"workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 27fbad579d8b4ebeacc6fd3ef7e85a39 +msgid "" +"[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" +"Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 a8791b670848474da292a467f01f8c45 +msgid "" +"[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." +"org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 fc20fa4c04104417b541a67ada2ab9a9 +msgid "" +"The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." +"replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 a93a7797a12b48dfa5bc3a7c50ab88e7 +msgid "" +"[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" +"Workflow_management_system)." +msgstr "" + +#: ../../src/setup.md:9 6f02fa47aca14c59a35b3ab750f5f236 +msgid "" +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. The information on this page has been migrated to the [FAQ](/faq." +"md) section of the new user guide." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 3821c2d16b254672a494522e47386cb0 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: 412a05f3492349a7bd26ea0c30e9bd80 +msgid "" +"Sometimes tools require additional command line options that don't " +"correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: 1232f6c81da141cb8482294eee5955dc +msgid "" +"In this example, we will wrap the Java compiler to compile a java source " +"file to a class file. By default, \"javac\" will create the class files in " +"the same directory as the source file. However, CWL input files (and the " +"directories in which they appear) may be read-only, so we need to instruct " +"\"javac\" to write the class file to the designated output directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: 485bb71673144e3f90f05b420b7079ac +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 0beb10c3133643f6b62c7d4aeec33709 +#: 5d48d9a2e977431f9a3625abaa466f5f +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: fcc1151a2e8b4a84b8595c7f913781a1 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 4a291c7ac7c84257b7402567d8364a36 +msgid "" +"And now invoke `cwltool` providing the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 3b1ae26038fd498ca0ae23aa70a35d3f +msgid "" +"Here we use the `arguments` field to add an additional argument to the " +"command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: 40388ebefb6947089c4a0f6d5d6e92e8 +msgid "" +"This example references a runtime parameter. Runtime parameters provide " +"information about the hardware or software environment when the tool is " +"actually executed. The `$(runtime.outdir)` parameter is the path to the " +"designated output directory. Other parameters include `$(runtime.tmpdir)`, " +"`$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and " +"`$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of " +"the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 a417fdd330db47a3aac07f7006c83ca9 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 99bad0fd9bee428a8d936d5a8e84d97d +msgid "" +"The following are a set of recommended good practices to keep in mind when " +"writing a Common Workflow Language description for a tool or workflow. These " +"guidelines are presented for consideration on a scale of usefulness: " +"although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 935500b0e6e249eba585644cddbd0253 +msgid "" +"No `type: string` parameters for names of input or reference files/" +"directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 96f924d6e02f4005b35d463e49be2982 +msgid "" +"A CWL document (in conjunction with any external components like " +"`Dockerfile`s) is software code. Workflow developers should be aware that " +"the usual rules of software licensing apply to this document. For example, " +"if the workflow is shared publicly, licensing terms must be clear so that a " +"future user understands under what conditions they can run the workflow, " +"modify it and/or combine it with other workflows. For this reason, please " +"consider including a license field in the document. The authors of this " +"guide urge you to choose a pre-existing license rather than trying to write " +"your own (see the link below to learn more about choosing a license), and " +"our recommended practice is to choose a license that allows for re-use by " +"anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 25e0a5c93ccc49bc8b6206c7c2e3de5c +msgid "" +"If possible, the license should be specified with its corresponding [SPDX " +"identifier][spdx]. Construct the metadata field for the license by providing " +"a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is " +"taken from the list of identifiers linked above. See the example snippet " +"below for guidance. For non-standard licenses without an SPDX identifier, " +"provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 34ad53bc5a40446daa0dac4571600d1e +msgid "" +"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" +"Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 4c397ffd2e9148e39bdd614683a98a78 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 1ed7f7e73afb4bd2ad2e29b65d020ff1 +msgid "" +"For more examples of providing metadata within CWL descriptions, see [the " +"Metadata and Authorship section of this User Guide](../topics/metadata-and-" +"authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 13b058dfa3cd4bbea54ae7d5a56c4c50 +msgid "" +"Include [attribution information][license-example] for the author(s) of the " +"CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" +"[orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 69369b917c1a45199343266650b1b220 +msgid "" +"In tool descriptions, list dependencies using short name(s) under " +"`SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 0245a61fd2ef4fb69cbb8d732086fb8f +msgid "" +"Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" +"identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 e9a56e3634a042279cae1745b7820658 +msgid "" +"All `input` and `output` identifiers should reflect their conceptual " +"identity. Use informative names like `unaligned_sequences`, " +"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " +"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 8a180861a66c4aaa9e8fdefd929ed829 +msgid "" +"In tool descriptions, include a list of version(s) of the tool that are " +"known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 00f333a383b64578b32c687b42924a77 +msgid "" +"`format` should be specified for all input and output `File`s. " +"Bioinformatics tools should use format identifiers from [EDAM][edam-" +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with " +"`$namespaces: { iana: \"https://www.iana.org/assignments/media-types/\" }`. " +"[Full IANA media type list][iana-types] (also known as MIME types). For non-" +"bioinformatics tools, use or build an appropriate ontology/controlled " +"vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 6b960d362bb540299f0560c14c5f2d8c +msgid "" +"Mark all input and output `File`s that are read from or written to in a " +"streaming compatible way (only once, no random-access), as `streamable: " +"true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 9cf9342bf0864e87b495913d8e06d021 +msgid "" +"Each `CommandLineTool` description should focus on a single operation only, " +"even if the (sub)command is capable of more. Don't overcomplicate your tool " +"descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 587b048324e447cb85844d8c64ae9a1e +msgid "" +"Custom types should be defined with one external YAML per type definition " +"for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 d8df6bbd5d324f7c9f48edb33e113b75 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 2235174088ad48a89d4fc21223e627b7 +msgid "" +"If useful, include a top-level `doc` as well. This should provide a longer, " +"more detailed description than was provided in the top-level `label` (see " +"above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 a0f0953a1a9f40cebd4dbe028784ff96 +msgid "" +"Use `type: enum` instead of `type: string` for elements with a fixed list of " +"valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 0ec380c683534892b6b8b8fcea84f765 +msgid "" +"Evaluate all use of JavaScript for possible elimination or replacement. One " +"common example: manipulating `File` names and paths? Consider whether one of " +"the [built in `File` properties][file-prop] like `basename`, `nameroot`, " +"`nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 65f23741db4e4a6abda8e5f7e036753a +msgid "" +"Give the tool description to a colleague (preferably at a different " +"institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 34c2caee8eb84e01a37033b67eb4aaba +msgid "" +"Complex workflows with individual components which can be abstracted should " +"utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " +"workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 d7c7484b2f1048aea9802400410f0858 +msgid "" +"Software containers should be made to be conformant to the " +"[\"Recommendations for the packaging and containerizing of bioinformatics " +"software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 a905abc2eead4dbaa035235936025499 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 eb91b6dab34d4d5f9854ac580a6cbde2 +msgid "" +"A command-line tool is a type of Process object that can be run by itself or " +"as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " +"etc. The command-line tool is defined in the `baseCommand` attribute of the " +"command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 7caeb91564634091a932f1270c4f5ef9 +msgid "" +"A CWL command-line tool must also have `inputs` and `outputs`. The following " +"example contains a minimal example of a CWL command-line tool for the `echo` " +"Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 c6ac4a60d102407991f40b892fb60560 +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 51d3ce421db345f5ab19e02fbbc51df2 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 8311d1430e624435b7b04bf2574a90c5 +msgid "" +"The example above uses a simplified form to define inputs and outputs. You " +"will learn more about in the [Inputs](../topics/inputs.md) and in the " +"[Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 d1c03e5f19d64ea89276d126de6e4bda +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 8494b43e98dd424db7d57aa1d731f7b4 +msgid "" +"This indicates whether a process requires outgoing IPv4/IPv6 network access. " +"If a command-line tool is written manually in CWL v1.1+, there is a need to " +"specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 8c4573fb120149269a0fe3a1ba6c9ef8 +msgid "" +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " +"Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: e1c709ac0fb249928d14aeced6551ae0 +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: c26c9c640e0747c8b2c2977c860c9d82 +msgid "" +"Sometimes you need to create a file on the fly from input parameters, such " +"as tools that expect to read their input configuration from a file rather " +"than the command line parameters, or need a small wrapper shell script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: edbe918d7df14cafb440e171e46c6de3 +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: 6d457d9b4ae746d384e65d9a37ca3591 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: 868394c1b8374ee6bbd43463e73d7edc +msgid "" +"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " +"expanded by the CWL engine before creating the file. Here, insert the value " +"at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 08a9e08cba674db09c9bfbef37e9579f +msgid "" +"The _CWL expressions_ are independent of any _shell variables_ used later " +"during command line tool invocation. That means that any genuine need for " +"the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` " +"above is expanded to `${PREFIX}` in the generated file to be evaluated by " +"the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 6f6f437753dd4eddae0b2ea62046fe39 +msgid "" +"To test the above CWL tool, use this job to provide the input value " +"`message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 +#: 096b17907bc3452d9927ef2fb6f5c11f 78ed5d8fb9bd4e068023d2c717e20f62 +#: c3a2e9e6b4414597a17db6d55d98e9d1 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: ac783e6415a44cb59d4b425bac5087b7 +msgid "" +"Before we run this, let us look at each step in a little more detail. The " +"base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: b9e6e15b541149c6a2d3922c11405267 +msgid "" +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML " +"array, we need a `-` on the first line of each element of the array, in this " +"case we have just one element. `entryname:` can have any value, but it must " +"match what was specified in the `baseCommand`. The final part is `entry:`, " +"this is followed by `|-` which is YAML quoting syntax, and means that you " +"are using a multiline string (without it, we would need to write the whole " +"script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 87088899567a4402aeb34605d3c6b06b +msgid "" +"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " +"formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 +#: 304c1bfe5ecd4d26b5dfaf9ad2e2c7f8 3ef7f0e3099147d78fd2d30bfa73cc6b +#: 4fef79a30282456eb9b5dd34a5eec0b1 afe775762ed348e5982b99bcf1451606 +#: f0689cd0e5b34414b6693331186ee4a3 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on the " +"command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 9f1967411aa7497fa43a4851f0645d6e +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 90bd62e4ef8b41e398a5c9b31f132774 +msgid "" +"Sometimes you may want to write your own custom types for use and reuse in " +"CWL descriptions. Use of such custom types can reduce redundancy between " +"multiple descriptions that all use the same type, and also allow for " +"additional customisation/configuration of a tool/analysis without the need " +"to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 3465527b8ff4407587f7c46fa9fa2a98 +msgid "" +"The example below is a CWL description of the [biom convert format][biom] " +"tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 c0cc869690804ada96a5c1813d17b895 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 01f369931c8142c08fe821a0ca31bf92 +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 0b3ff704cdea44e28aee3c704ca98e27 +msgid "" +"___Note:___ To follow the example below, you need to [download the example " +"input file](https://github.com/common-workflow-language/user_guide/blob/main/" +"src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), " +"*rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 cb456bcae0dd41ffbc514eeea283e130 +msgid "" +"On line 29, in `inputs:table_type`, a list of allowable table options to be " +"used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 c610173365d04c57900b22f4024b47b4 +msgid "" +"The reference to a custom type is a combination of the name of the file in " +"which the object is defined (`biom-convert-table.yaml`) and the name of the " +"object within that file (`table_type`) that defines the custom type. In this " +"case the `symbols` array from the imported `biom-convert-table.yaml` file " +"define the allowable table options. For example, in `custom-types.yml`, we " +"pass `OTU table` as an `input` that tells the tool to create an OTU table in " +"hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 c2b2e18d55c94721812431583cfc4725 +msgid "" +"The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 3e61c3920a7a45db8917c348bd44384d +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 cd87d210b03c4da2a7608b40a6bbcca0 +msgid "" +"In order for the custom type to be used in the CWL description, it must be " +"imported. Imports are described in `requirements:SchemaDefRequirement`, as " +"below in the example `custom-types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 7af9ba3219e44ed49b8da781db5d6fb5 +msgid "" +"Note also that the author of this CWL description has also included " +"`ResourceRequirement`s, specifying the minimum amount of RAM and number of " +"cores required for the tool to run successfully, as well as details of the " +"version of the software that the description was written for and other " +"useful metadata. These features are discussed further in other chapters of " +"this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 eae1994f3a4d481b863b5125c7f4a383 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 8bd8c06d416740b69d126eb9f5f24ad3 +msgid "" +"Tools run in a restricted environment and do not inherit most environment " +"variables from the parent process. You can set environment variables for " +"the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 11c6bffc620b4c789b29ab4034a8bfbd +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 89888b1b994546ce8a93f9630b4bb07e +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 191d3010b9244b39bc3bc50246ac7ad7 +msgid "" +"An expression tool is a type of Process that can be run by itself or as a " +"Workflow step. It executes a pure JavaScript expression. It is meant to be " +"used as a way to isolate complex JavaScript expressions that need to operate " +"on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 3437ed6e184748e4af1ef62f32c8cef1 +msgid "" +"Similar to the command-line tool it requires `inputs` and `outputs`. But " +"instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 c3ae1ef318bb4e0fada76c353dd5f6f1 +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 a7f5e04d242c48a7b3deffb5ff6528be +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 32b6841faed044409bc618cba54a22f0 +msgid "" +"We had to use an `InlineJavascriptRequirement` as our expression contains a " +"JavaScript call in `.toUpperCase()`. This means to tools using the " +"expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 6821ba7a84a44d309d245c429948ad09 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 8167269bc3a64c72bd6c909362350a15 +msgid "" +"If you need to manipulate input parameters, include the requirement " +"`InlineJavascriptRequirement` and then anywhere a parameter reference is " +"legal you can provide a fragment of Javascript that will be evaluated by the " +"CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 c0f75603a6024063a6911f17c70908cc +msgid "" +"JavaScript expressions should only be used when absolutely necessary. When " +"manipulating file names, extensions, paths etc, consider whether one of the " +"[built in `File` properties][file-prop] like `basename`, `nameroot`, " +"`nameext`, etc, could be used instead. See the [list of best practices](best-" +"practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 7faec63b389a4c07b6929b7a78f0cc70 +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 d7dca89942f949d58cb18cb94bb7de72 +msgid "" +"As this tool does not require any `inputs` we can run it with an (almost) " +"empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 1abc1a21c0764415b138099e0e21432b +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 b8b5a50a82e44e49a37c6396f1ff9464 +msgid "" +"`empty.yml` contains a description of an empty JSON object. JSON objects " +"descriptions are contained inside curly brackets `{}`, so an empty object is " +"represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 b38d66c12ab74dfc9395e69d9c04bbf5 +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 8417aa7a9d034361a41def6b71e93413 +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 c1f672b377da4605b9c5098ebb6e1147 +msgid "" +"Note that requirements can be provided with the map syntax, as in the " +"example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 af52f5197e8545d2be22cc0f7f03648c +msgid "" +"Or as an array, with each entry (in this case, only `class: " +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " +"describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 5e12ce15018942bf9010ce6519c17b00 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 e2e9c5f7b681427a9589476649e5a9d8 +msgid "" +"Just like [parameter references](parameter-references.md), you can use " +"JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 8a74763ead0147bbaf3892e552fad546 +msgid "" +"From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 0aab7de8d69f49438d4eeed17316df68 +#: 75f90cb870d14d0dbb4c4ee80d32a65e +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 0b9d8268c177489b86b8eaa638dfa063 +#: 204cd6d8375a4462a8247863a96df906 2b7e56ceb4ad49a8b29a58b10bad7c0a +#: 81f15c64379941d8ac2a681b3879761c f11ae7d801db45989b598864dc6291c9 +#: fc4534b475334f7281d1740c9a78f640 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 70e9085b21f640d6893309a3375c0511 +#: f529003dd7a64bc7be0ccef8dbfa84b3 +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 3fceb522ba6245129b826c342eaf31b4 +#: a5f71add5b8345a4bfa02853ef8a6d35 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 018300196ea24550988a0156894b5e85 +#: 2c799286e8204ed9a83c3fc006988139 +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 25d91d6624bd42e7948e29c684e8e441 +msgid "" +"From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 0944d6525c3c460aa4b5a0e72552ca4d +#: 1187b0d330cb470fbea82a8b8c95aa28 265602307ccd42458ba47ac1b689242c +#: 2febce1b1ad74b18af3a9b3fa137c780 3215ee41f96541cbbda60a1167386c2f +#: 80efeab6ec0e447bbe158cbaa57f83d8 8d2bbd91b4ab4faa923fc1a14ec49dd5 +#: b4a6e640275b4fc7a18e3083e86b72a1 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 480b2e4207574b27b8d33dfe5e9ab64e +#: 4b4149a3b97a4de5b2d7fd84bd547ffe 7af1a82df41e40d0a430babafe1bc5e2 +#: be01787b66e34074af32bb45dcce8657 be099ab533504a7596fd56ec1ce7ca5d +#: c8b96271665444608f601a460dd28fb3 cb6dfa7bc68b41929a5247d929c2f94a +#: f7f452e92f6d4a14ba3912c62699019a +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 4811c1b9867b44caa70dec4b91970484 +msgid "" +"From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 0b1f2a8986e0419a90e484d3a945a037 +msgid "" +"From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 dbc02876870d49d2b9e39db4133a0f62 +msgid "" +"From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 97339a3fa43849f7b292f4643b5fe35c +#: da8b81b1e1884406a188fb04825ef90e +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 077e7b0d2dde443699050af8c63ab912 +#: c8cbe3dfd0984221ae72012ea26edc6f +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 3f07f4a8594640c2b2da4da521872b59 +#: 573f7e4b72ec4c47ab2e54e2c4877d9c +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 f03011b3479b47c690604c508d95c263 +msgid "" +"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" +"v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 1ec3f913909b4e04bb602767d23bd85d +#: 2f7130500b8c450fa4af226b18e38407 +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 a5849a856a374cda807ecf48034af915 +msgid "" +"From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 bd8bbd60aaff4e7aacec91bcbad500f4 +#: f0c99004211e4adf8c0b524d5bbcc12b +msgid "" +"From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." +"html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 96c544cf213245cfb3d1f5196223c6cc +#: c6a04d4f3ef24104b0a86f9093935c13 +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 946e0437a48b4d5da2a29d489250cbaa +msgid "" +"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](https://www." +"commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 1f287ebf87ae4e93bd1ac65cc1d01bf4 +msgid "" +"From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 0d0f4f0e12174d588c131afef70efc5f +#: a74e0e3499d644b4a9d999d3555f03de +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 b2e31c38f7cb4ecabd6b9b89ef051c0e +#: ddc9d9ae72a64a76a2a8e2bba22584ee +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 12f86817dfc14f2bb39509886d56017f +#: 8a94f2c3b1674162a268f67935a3025b +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 a800acfefb3f433fae2cdda9ac4a795a +#: bcb58fc2447a4472b86913871b8c12ee +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 5be337d412ba4d48877e991d535e810c +#: e6cf2f8498db4f549193be20d87e16f9 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 3bc61c8197664f12a98d1ac38b421b38 +#: 9973a87f747445ad89ce959420cac5fd +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 0f5dc4f5a4c64f818e2e22f20472ae84 +#: 2ec9d1f191f44686b1cb8622336d6b92 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 5382ff97ad2f419dbe1bed266997aa84 74406f77013443f28d4d6306c54b0df1 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 f594a20dc038457e815dc17bae6e031d +msgid "" +"From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 5814f96ee4ec4822aecad33c8eda0473 c46c44268b2a4b96b1df13e53e82e54c +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 b9824103ef8745bab30b65887c82f62f +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: 28b23f84c64549e7a0fe444ccc3e1b05 fdd5d742a6764e5db2281ed844bf3475 +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: b6123c911c804f3c8cb596d2aa495b2b d81a7d8b7db444409b286e5f1d863968 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: eb6255a0f8d748588d87e7ad38e507bd fffc5a80bd68495396d32b7a1821eb4e +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 b00a8a2a572742e0929470550433e929 +msgid "" +"From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 9b34c95e483e47f3828e79bf929a23b4 c968eebaf0114b23b789e9ce68e7588d +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 7c8fb996d1af4cfdb0d49d8ed2696745 +msgid "" +"Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 75a29e9ff2cf4b5bb6afa87a741a111b +msgid "" +"The requirement `InlineJavascriptRequirement` supports an `expressionLib` " +"attribute that allows users to load external JavaScript files, or to provide " +"inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 5233d8baa8b74391bf8fee5ae2324234 +msgid "" +"Entries added to the `expressionLib` attribute are parsed with the " +"JavaScript engine of a CWL runner. This can be used to include external " +"files or to create JavaScript functions that can be called in other parts of " +"the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 343e8b78a1f94b8cbafac05212e5a333 +msgid "" +"The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl." +"org/v1.0/CommandLineTool.html#Expressions) that the only version of " +"JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-" +"international.org/5.1/). This means that any code that you include or write " +"in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 0657ee8f03d8462ca6ca6fc538386b0d +msgid "" +"For example, we can use `InlineJavascriptRequirement` and write a JavaScript " +"function inline in `expressionLib`. That function can then be used in other " +"parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 e3c593cf50da426f8d9df215c7db0bc9 +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 b971e53c3ed847f1b7c7a6d50e344baf +msgid "" +"Running this CWL workflow will invoke the JavaScript function and result in " +"the `echo` command printing the input message with capital initial letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 d2315d46369f4e9d9c871d7f88f7006e +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 04fdaa45a7ed47d5830181611bda924e +msgid "" +"Let's move the `capitalizeWords` function to an external file, `custom-" +"functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 8d7686f62f314d98aae8c262befd5283 +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 e68ee17607be4a06a66f9fc67624aff5 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 76b85d3729274fc08adfadcbf1172650 +msgid "" +"The `custom-functions.js` file is included in the CWL document with the " +"`$include: custom-functions.js` statement. That makes the functions and " +"variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 29f334957fa940c289f385160cca6d63 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 6d255ae6b92a48fa9b7b98443cc2f5bb +msgid "" +"Finally, note that you can have both inline and external JavaScript code in " +"your CWL document. In this final example we have added another entry to the " +"`expressionLib` attribute with the new function `createHelloWorldMessage`, " +"that calls the `capitalizeWords` function from the external file `custom-" +"functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 89734e7855654b2e8bfddeea96241539 +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 1915f8e68f624027827d28f8e17d2dec +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 750f94edb4f84e45a276f6ab28fad95e +msgid "" +"The `$include` statement can be used to include a file from the local disk " +"or from a remote location. It works with both relative and absolute paths. " +"Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad." +"html#Include) from the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 2e9e8cfaf48a43a88c31a855dac4f748 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 c574b54d998243f28d2caa91434968a7 +msgid "" +"Tools and workflows can take `File` types as input and produce them as " +"output. We also recommend indicating the format for `File` types. This helps " +"document for others how to use your tool while allowing you to do some " +"simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 b0ec34507eea473c91d6ada09a1c5c09 +msgid "" +"For file formats, we recommend referencing existing ontologies (like EDAM in " +"our example), reference a local ontology for your institution, or do not add " +"a file format initially for quick development before sharing your tool with " +"others. You can browse existing [IANA file format listings][IANA] and [EDAM " +"file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 a688e39859734a518c0fcc19f532a432 +msgid "" +"In the next tutorial, we explain the `$namespaces` and `$schemas` section " +"of the document in greater detail, so don't worry about these for now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 e068422ad9b84ca1b27008127928cc0f +msgid "" +"Note that for added value `cwltool` can do some basic reasoning based on " +"file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 8c3ef5e145b14299bf3671add0da56ac +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: 0d92f1c0f1ce448fb698e9b390b45c15 fc4773204ebc4e3789bb076dff0d0393 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 900abc5aa6a940f48f9c93e79cd1c47f +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 0390555b96c84aadbd9325c152972087 +msgid "" +"Below is an example of a parameter file for the example above. We encourage " +"checking in working examples of parameter files for your tool. This allows " +"others to quickly work with your tool, starting from a \"known good\" " +"parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 d5752ee5437b496ca10f4f12b76fc5dc +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 91dc76bb4565473ab948eecf628a405c +msgid "" +"___Note:___ To follow the example below, you need to download the example " +"input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 0b8b9b7f533543a49f876421ce6057d9 +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 1b6cfac3a92347d4b98bb54de1e26870 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 53dd5f476f064cbf9b9826d1e80eb830 +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 420b33d143fc44d1b237bc678f0af663 +msgid "" +"The `inputs` of a tool is a list of input parameters that control how to run " +"the tool. Each parameter has an `id` for the name of parameter, and `type` " +"describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 55136332e3bb48f892cf6a74c67a4ac6 +msgid "" +"Available primitive types are *string*, *int*, *long*, *float*, *double*, " +"and *null*; complex types are *array* and *record*; in addition there are " +"special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 cb2527899cc04b6d8060c4d57883beb5 +msgid "" +"The following example demonstrates some input parameters with different " +"types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 c79668b856b14243b4fad0f46dc5d6d7 +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 ed6f3e5c7b3f403a9a94359983107645 +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 034075eb09db4897a96d3332408427db +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 08181d391cc543a5a81d3257654df213 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 15215522e38242c4b17ec3aa089269d4 +msgid "" +"You can use `cwltool` to create a template input object. That saves you from " +"having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 64bd3382ec234ec8a50217b794b96916 +msgid "" +"You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " +"> inp-job.yml`, and then modify the default values with your desired input " +"values." +msgstr "" + +#: ../../src/topics/inputs.md:44 3611c1ca498a4197a4a6612c60f5f565 +msgid "" +"Notice that \"example_file\", as a `File` type, must be provided as an " +"object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 da924e8142d34e86bcb5de1cd1da71ca +msgid "" +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " +"command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 13c97256a5ee49c99f4010edf9dbc9bf +msgid "" +"Now invoke `cwltool` with the tool description and the input object on the " +"command line, using the command `cwltool inp.cwl inp-job.yml`. The following " +"boxed text describes these two commands and the expected output from the " +"command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 dcc3f2a47a6449efb857af63ed4b65d0 +msgid "" +"The CWL reference runner (cwltool) and other runners create temporary " +"directories with symbolic (\"soft\") links to your input files to ensure " +"that the tools aren't accidentally accessing files that were not explicitly " +"specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 cf54a30ae24f4013bb19f379a7ca67be +msgid "" +"The field `inputBinding` is optional and indicates whether and how the input " +"parameter should appear on the tool's command line. If `inputBinding` is " +"missing, the parameter does not appear on the command line. Let's look at " +"each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 ff75644bae9c46af8379d78360d4c696 +msgid "" +"Boolean types are treated as a flag. If the input parameter " +"\"example_flag\" is \"true\", then `prefix` will be added to the command " +"line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 e90abe59a84e48d4b8d6caa737e087aa +msgid "" +"String types appear on the command line as literal values. The `prefix` is " +"optional, if provided, it appears as a separate argument on the command line " +"before the parameter . In the example above, this is rendered as `--example-" +"string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 9275236d87b646cab1058dd750e11a50 +msgid "" +"Integer (and floating point) types appear on the command line with decimal " +"text representation. When the option `separate` is false (the default value " +"is true), the prefix and value are combined into a single argument. In the " +"example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 6a39929af73f4ba9b6455ed9fd287e08 +msgid "" +"File types appear on the command line as the path to the file. When the " +"parameter type ends with a question mark `?` it indicates that the parameter " +"is optional. In the example above, this is rendered as `--file=/tmp/random/" +"path/whale.txt`. However, if the \"example_file\" parameter were not " +"provided in the input, nothing would appear on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 44ce716561cc4dff8fef1ca59f816c7c +msgid "" +"Input files are read-only. If you wish to update an input file, you must " +"[first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 9f1da592350f40ee88920465e2004148 +msgid "" +"The value of `position` is used to determine where parameter should appear " +"on the command line. Positions are relative to one another, not absolute. " +"As a result, positions do not have to be sequential, three parameters with " +"positions 1, 3, 5 will result in the same command line as 1, 2, 3. More " +"than one parameter can have the same position (ties are broken using the " +"parameter name), and the position field itself is optional. The default " +"position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 5116d91f247f44518eb21840415f6eaa +msgid "" +"The `baseCommand` field will always appear in the final command line before " +"the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 08b26d1688e3470288e73d587f052d88 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 f91994a4279a41bda3de41fe79008c62 +msgid "" +"It is easy to add arrays of input parameters represented to the command " +"line. There are two ways to specify an array parameter. First is to provide " +"`type` field with `type: array` and `items` defining the valid data types " +"that may appear in the array. Alternatively, brackets `[]` may be added " +"after the type name to indicate that input parameter is array of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 4b93a4f980634e88a8f34a38703fc906 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 de3e760ebb0e4ae099deddb978046a2c +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 06ec811e8f0e43b8b929198533ac8082 +#: 797c06f0605d4e4ba306c2803a7834f9 d76d42c490a24b6daed944f45fe7a351 +msgid "" +"Now invoke `cwltool` providing the tool description and the input object on " +"the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 49406f30f62346968bb1250efc940f70 +msgid "" +"The `inputBinding` can appear either on the outer array parameter definition " +"or the inner array element definition, and these produce different behavior " +"when constructing the command line, as shown above. In addition, the " +"`itemSeparator` field, if provided, specifies that array values should be " +"concatenated into a single argument separated by the item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 3d8711f0135e4ab1b59fce94c83b97c0 +msgid "" +"Note that the arrays of inputs are specified inside square brackets `[]` in " +"`array-inputs-job.yml`. Arrays can also be expressed over multiple lines, " +"where array values that are not defined with an associated key are marked by " +"a leading `-`. This will be demonstrated in the next lesson and is discussed " +"in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify " +"arrays of arrays, arrays of records, and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 6f146779d6a84888948751b8b1fd0515 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 e5970a83876e4b5e9a02f2ab0030eb83 +msgid "" +"Sometimes an underlying tool has several arguments that must be provided " +"together (they are dependent) or several arguments that cannot be provided " +"together (they are exclusive). You can use records and type unions to group " +"parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 0db71b22173846d7b8d4aeb66d2ed8ed +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 f90fd48656a7424aac304987adf1b068 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 3c8bd9134a1c4bda9461362df3257d6b +msgid "" +"In the first example, you can't provide `itemA` without also providing " +"`itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 63bd06780bb949e5b1a1d10389c8c23f +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 0d448baa57f14e7783d3167611e8c659 +msgid "" +"In the second example, `itemC` and `itemD` are exclusive, so only the first " +"matching item (`itemC`) is added to the command line and remaining item " +"(`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 202239a6e90044e39b676d641aa6d58a +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 512ecb3349b0450cb741de4ed2d2e850 +msgid "" +"In the third example, only `itemD` is provided, so it appears on the command " +"line." +msgstr "" + +#: ../../src/topics/inputs.md:255 185ff0bb49e841c592b29112eb171bdc +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 6cd5df09e4594d78a526f199ac577881 +msgid "" +"If you use exclusive input parameters combined with expressions, you need to " +"be aware that the `inputs` JavaScript object will contain one of the " +"exclusive input values. This means that you might need to use an **or** " +"boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 9db9f784a5cd4ca5b90691d1e2e827ea +msgid "" +"Let's use an example that contains an exclusive `file_format` input " +"parameter that accepts `null` (i.e. no value provided), or any value from an " +"enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 09b1db3cc6c845058cf0ad4c24d71733 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 84aa6e0c479f4528836691005129056e +msgid "" +"Note how the JavaScript expression uses the value of the exclusive input " +"parameter without taking into consideration a `null` value. If you provide a " +"valid value, such as “fasta” (one of the values of the enum), your command " +"should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 76611ebb19764bdc8a1f6eacfb76138f +msgid "" +"However, if you do not provide any input value, then `file_format` will be " +"evaluated to a `null` value, which does not match the expected type for the " +"output field (a `string`), resulting in failure when running your workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 bf9750d215be4294b1cf1e0490a0796a +msgid "" +"To correct it, you must remember to use an or operator in your JavaScript " +"expression when using exclusive parameters, or any parameter that allows " +"`null`. For example, the expression could be changed to `$(inputs." +"file_format || 'auto')`, to have a default value if none was provided in the " +"command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: 612f9efa0ed04559a174c37958def6f7 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: 57eb990c11f044dfb60c012a92a30eb1 +msgid "" +"Implementation extensions not required for correct execution (for example, " +"fields related to GUI presentation) and metadata about the tool or workflow " +"itself (for example, authorship for use in citations) may be provided as " +"additional fields on any object. Such extensions fields (e.g. `format: edam:" +"format_2572`) can use a namespace prefix listed in the `$namespaces` section " +"of the document (e.g. edam: http://edamontology.org/) as described in the " +"[Schema Salad specification][schema-salad]. Once you add the namespace " +"prefix, you can access it anywhere in the document as shown below. " +"Otherwise, one must use full URLs: `format: http://edamontology.org/" +"format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: a6e6155cb8ff40fb9d8b1fff3e94fb02 +msgid "" +"For all developers, we recommend the following minimal metadata for your " +"tool and workflows. This example includes metadata allowing others to cite " +"your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 063c28fc9e654dfd91c66da164ac1d3d +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: 8fcd2ae1ce8d4c7f951281ced81ab32d +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: 639533652456427480fa311da7beb4f0 +msgid "" +"For those that are highly motivated, it is also possible to annotate your " +"tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints at " +"hardware requirements in order to use the tool, and a few more metadata " +"fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 266808daf2004bbd9830045fbc67a541 +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 fd9b715bfa3243b19a919ad19843232d +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 fb568063fa7a4cbe83c271772d3d62bc +msgid "" +"An Operation is a type of CWL process, just like a workflow, a command-line " +"tool, or an expression tool. It is a step of a workflow that specifies " +"inputs and outputs, but it does not provide enough information to be " +"executed." +msgstr "" + +#: ../../src/topics/operations.md:7 981486166754435cbcd8152e93679405 +msgid "" +"You can create operations to visualize a workflow during development, before " +"you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 7b165718ffeb42e793c97fad807f216f +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 5e31cddd14414d31b7bd0a6c2745d272 +msgid "" +"The `uppercase` step of the workflow is an operation. It can be used like a " +"command line tool or an expression. You can also plot it with the CWL Viewer " +"or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 02c372245dc9453ea0841026335e405b +msgid "" +"The output of the command above can be rendered with a Graphviz renderer. " +"The following image is rendered with the Sphinx Graphviz directive (this " +"user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 d331327285d1434e8c17187737345919 +msgid "" +"If you try running it with `cwltool`, the command will fail since `cwltool` " +"does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 72705f8940bb4194bc5554fcc29eed49 +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 76b7c63107e94323859904415d07d31c +msgid "" +"CWL runners may come up with ways to bind operations to concrete steps. A " +"CWL runner could, for instance, use abstract operations with ID's that " +"correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 ebf56d267612461799bf801136e61b69 +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 f9cff6b272a24ef6ada90e263c1b1784 +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 e482821911004cdd8c3ff1539c69368a +msgid "" +"The `outputs` of a tool is a list of output parameters that should be " +"returned after running the tool. Each parameter has an `id` for the name of " +"parameter, and `type` describing what types of values are valid for that " +"parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 e11fcfe1e84b476ea879810b76ff2cb8 +msgid "" +"When a tool runs under CWL, the starting working directory is the designated " +"output directory. The underlying tool or script must record its results in " +"the form of files created in the output directory. The output parameters " +"returned by the CWL tool are either the output files themselves, or come " +"from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 65c73a37f06a4782bf43f4acf4f1c77e +msgid "" +"The following example demonstrates how to return a file that has been " +"extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 e172dde545164fefac826d910ddd399e +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 225f4d04c28149898f06bd771f741358 +msgid "" +"In previous examples, the `baseCommand` was just a string, with any " +"arguments passed as CWL inputs. Instead of a single string we can use an " +"_array of strings_. The first element is the command to run, and any " +"subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 14e9e446768a454ea786b3256b49632e +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 4bd659cee1904868a7c33345f94f1300 +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 8803a28ccff846eea7d06f4bd908c763 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 661b62e554d64e449c69e475e5188f99 +msgid "" +"And now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 44cdca5b777441baa246c87940df7264 +msgid "" +"The field `outputBinding` describes how to set the value of each output " +"parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 edb34af3b22d418d9a6178c0ecbb8b80 +msgid "" +"The `glob` field consists of the name of a file in the output directory. If " +"you don't know name of the file in advance, you can use a wildcard pattern " +"like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 10e68fad866f4187981f0b365b957b03 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 77e1261484964ba9ac67d9fc9139a1d6 +msgid "" +"To capture a tool's standard output stream, add the `stdout` field with the " +"name of the file where the output stream should go. Then add `type: stdout` " +"on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 c66bd08354d54ccb9e3e1da89634a816 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 7d4056355da1451dbed6733fba8c3c38 +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 8fed80f9633a4e87a67c651dc3160ce6 +msgid "" +"You can also capture multiple output files into an array of files using " +"`glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 6cba36e037d54f93add05fb16d2359bd +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 08862892ecf849a1ba2f25ecc9e98227 +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 c5dcc68bb28041b3b96ac1af716b0db8 +msgid "" +"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " +"expected outputs is specified in `array-outputs-job.yml` with each entry " +"marked by a leading `-`. This format can also be used in CWL descriptions to " +"mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 53b95fd10d61462daf153d45e5517dad +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 0702e71de81e493dac08a91d667569e3 +msgid "" +"In a previous example, we extracted a file using the \"tar\" program. " +"However, that example was very limited because it assumed that the file we " +"were interested in was called \"hello.txt\", and this was written into the `." +"cwl` file. This is not the best way to do this, as the \"hello.txt\" " +"filename may vary or be dependent on the input file(s) used. To avoid this " +"we can specify the name of the file we want in the job parameters file (`." +"yml`). In this example, you will see how to reference the value of input " +"parameters dynamically from other fields, which will allow us to then " +"specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 a1703da32ad64fd2b8bdd423605b50bd +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 2f32531e47b4465594d41ddd218fb2fd +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 501dd6f9dbb1438f9a59f6a025639f35 +msgid "" +"Create your input files and invoke `cwltool` with the tool description and " +"the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 1bcdd99111bd4bc5b75a8297bb61d9bb +msgid "" +"Certain fields permit parameter references which are enclosed in `$(...)`. " +"These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 32eae36c593e43a9a6b4e103a0c2028a +msgid "" +"References are written using a subset of Javascript syntax. In this " +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " +"`$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 1d785e8a450140a982142aa0fa906257 +msgid "" +"The value of the \"inputs\" variable is the input object provided when the " +"CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 e862bb8bc3e84e24a2aa5ec34298cfd5 +msgid "" +"Note that because `File` parameters are objects, to get the path to an input " +"file you must reference the path field on a file object; to reference the " +"path to the tar file in the above example you would write `$(inputs.tarfile." +"path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 46ffaab11be040cea96a294d9a814738 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 890d619c415741179c83ffcd56833fbe +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 373e1847d9f745d7a749928642c8e0e3 +msgid "" +"From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 90d3624e062c41c7a6d1a9824515d0df +msgid "" +"From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 76d09490bd464b708c28991dbff0104e +msgid "" +"From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 f33c76e590dd4feaac1e3cf568069d33 +msgid "" +"From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 74ed4a06c1984c58826ddceb1a45a4ea +msgid "" +"From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 eba3362d34354daa89dc516722c6fbd0 +msgid "" +"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" +"v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 e924874af32d4be19c5e8446768226dd +msgid "" +"From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 b162113f364445af9ff1bfc8a6610e13 +msgid "" +"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." +"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 aa721077e16948c3a5bb8ef5bd7aff04 +msgid "" +"From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 2fad0c2bc2834350826b22c454d33cf0 +msgid "" +"From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: 9e303aa89a9b4447b0dbdc5ac0a0eb9e +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: 7a4eb47c25a54d11a00eb73e9333ad1c +msgid "" +"From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: 8a957bc8e577476bb59647661b3c0990 +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: 2b31f1dec3f5498e9e363a4f1f50dc8d +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 5a5f84ecc2f449bf9f037dc9da0ac670 +msgid "" +"Often, tool descriptions will be written for a specific version of a " +"software. To make it easier for others to use your descriptions, you can " +"include a `SoftwareRequirement` field in the `hints` section. This may also " +"help to avoid confusion about which version of a tool the description was " +"written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: ee89f1526c1f4452b4e36ba67bb59747 +msgid "" +"In this example, the software requirement being described is InterProScan " +"version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: c76cec44f5424f6087df28aa33c521a2 +msgid "" +"Depending on your CWL runner, these hints may be used to check that the " +"required software is installed and available before the job is run. To " +"enable these checks with the reference implementation, use the [dependency " +"resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 072d7b3ce3284ed994ff0736b43bbb86 +msgid "" +"As well as a version number, a unique resource identifier (URI) for the tool " +"is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked " +"up in the [SciCrunch][scicrunch] registry, which provides a portal for " +"finding, tracking, and referring to scientific resources consistently. If " +"you want to specify a tool as a `SoftwareRequirement`, search for the tool " +"on SciCrunch and use the RRID that it has been assigned in the registry. " +"(Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool " +"to SciCrunch). You can use this RRID to refer to the tool (via [identifiers." +"org][identifiers]) in the `specs` field of your requirement description. " +"Other good choices, in order of preference, are to include the DOI for the " +"main tool citation and the URL to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 395d611104604a28b78e11b112a95027 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 811b4db0b1794fa89dc870f6cb59a3cd +msgid "" +"Normally, input files are located in a read-only directory separate from the " +"output directory. This causes problems if the underlying tool expects to " +"write its output files alongside the input file in the same directory. You " +"use `InitialWorkDirRequirement` to stage input files into the output " +"directory. In this example, we use a JavaScript expression to extract the " +"base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 7159b5c5023c47128057c4116cce69f4 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 3bfa6791d78f43629de90345f4441ebb +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 9a6bd5b684a740ed9e8993d9f8607774 +msgid "" +"In this section you will find ways to troubleshoot when you have problems " +"executing CWL. We focus on `cwltool` here but some of these techniques may " +"apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 6db8a02139644598894220d538c590b9 +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 f0da0f6283d44bcc95224eb9fe2d1764 +msgid "" +"You can use the `--cachedir` option when running a workflow to tell " +"`cwltool` to cache intermediate files (files that are not input nor output " +"files, but created while your workflow is running). By default, these files " +"are created in a temporary directory but writing them to a separate " +"directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 e2fc28b44ffe4254892a7c7973dc80c4 +msgid "" +"In the following example `troubleshooting-wf1.cwl` we have two steps, " +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | " +"rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW " +"olleH\". However, the second step, `step_b`, **has a typo**, where instead " +"of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 505c7cf9ee9c4af1aeed29002eed1b33 +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 4c31fd11a28943538690d04baa2b5dd0 +msgid "" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " +"(`cwltool` will create the directory for you if it does not exist already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 a8532ac700014db4bd8ef690a27fb844 +msgid "" +"The workflow is in the `permanentFail` status due to `step_b` failing to " +"execute the non-existent `revv` command. The `step_a` was executed " +"successfully and its output has been cached in your `cachedir` location. You " +"can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 94a6148512b24b90b87fd1312a926d75 +msgid "" +"Each workflow step has received a unique ID (the long value that looks like " +"a hash). The `${HASH}.status` files display the status of each step executed " +"by the workflow. And the `step_a` output file `stdout.txt` is visible in the " +"output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 ec4165b7c25c449db6a8804161805e80 +msgid "" +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in " +"the `step_b`). After fixing the typo, when you execute `cwltool` with the " +"same arguments as the previous time, note that now `cwltool` output contains " +"information about pre-cached outputs for `step_a`, and about a new cache " +"entry for the output of `step_b`. Also note that the status of `step_b` is " +"now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 5c0b71a6376848d4aa491854ea2d185d +msgid "" +"In this example the workflow step `step_a` was not re-evaluated as it had " +"been cached, and there was no change in its execution or output. " +"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " +"`step_b` after we fixed the executable name. This technique is useful for " +"troubleshooting your CWL documents and also as a way to prevent `cwltool` to " +"re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 95b832552e8443ea9c652f8c95afc01e +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 561fc9c561bc492ea82c17784dfd439c +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 2420b16855cf4b25af5bcb87413f6dd9 +msgid "" +"[Docker][docker] containers simplify software installation by providing a " +"complete known-good runtime for software and its dependencies. However, " +"containers are also purposefully isolated from the host system, so in order " +"to run a tool inside a Docker container there is additional work to ensure " +"that input files are available inside the container and output files can be " +"recovered from the container. A CWL runner can perform this work " +"automatically, allowing you to use Docker to simplify your software " +"management while avoiding the complexity of invoking and managing Docker " +"containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 f5266ee2c2b34170bc89cb501b869893 +msgid "" +"One of the responsibilities of the CWL runner is to adjust the paths of " +"input files to reflect the location where they appear inside the container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 728166bf41504e1d89b755400742a1b4 +msgid "" +"This example runs a simple Node.js script inside a Docker container which " +"will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 104351ac29d247cb8e017228e2c9b3d8 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 e11a38bfb30b404c99d223647960cb16 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 7ed0bd21e998417cb02fdcb8e44734b6 +msgid "" +"Before we run this, let's just break it down and see what some bits do. " +"Most of this has been explained in previous sections, the only part that is " +"really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 9dcddf6812ba4bc2a7d6c5fcdb978a68 +msgid "" +"`baseCommand: node` tells CWL that we will be running this command using the " +"Node Js runtime that is meant for Javascript files. We then need to specify " +"some `hints` for how to find the container we want. In this case we list " +"just our requirements for the docker container in `DockerRequirements`. The " +"`dockerPull:` parameter takes the same value that you would pass to a " +"`docker pull` command. That is, the name of the container image (you can " +"even specify the tag, which is good idea for best practices when using " +"containers for reproducible research). In this case we have used a container " +"called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 bc1a09475f154562a4db445bf81ac92f +msgid "" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " +"the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 2e117019ace84604a8ed5a31214c2587 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 d0d5b2a1a008411e92859a72101088c1 +msgid "" +"Notice the CWL runner has constructed a Docker command line to run the " +"script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 591d1cd0282b4095a267b44da7d59804 +msgid "" +"In this example, the path to the script `hello.js` is `/home/me/cwl/" +"user_guide/hello.js` outside the container but `/var/lib/cwl/" +"job369354770_examples/hello.js` inside the container, as reflected in the " +"invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 9f989fff165448ecbcaad6adc0f58d6b +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 212c82dca23645e89d8b5bb7599f2d25 +msgid "" +"A workflow is a CWL processing unit that executes command-line tools, " +"expression tools, or workflows (sub-workflows) as steps. It must have " +"`inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 7530029ec04746f2a888dcbc10aa5ce4 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 c1f1d644b37b4f018b87e15249d8758d +msgid "" +"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " +"command-line tool, and the expression tool showed in the earlier examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 2d07232b7d9c415b8ad971e8cbcd9577 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 fa1f770ffeba4b74bcb200cd3949e070 +msgid "" +"A command-line tool or expression tool can also be written directly in the " +"same CWL document as the workflow. For example, we can rewrite the `echo-" +"uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 570020792e824c2ba732bcc2c0134aa1 +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 8a50c511004941d0917a8f0d471467f0 +msgid "" +"Having separate files helps with modularity and code organization. But it " +"can be helpful writing everything in a single file for development. There " +"are other ways to combine multiple files into a single file (e.g. `cwltool --" +"pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 4d2bf0341836405d9729c47d8020faea +msgid "" +"For a sub-workflows you need to enable the requirement " +"`SubworkflowFeatureRequirement`. It is covered in another section of this " +"user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 dd6fc85f74984517b284853a0d46c122 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 f857d80cd5d84622a560c895ab260a92 +msgid "" +"This workflow extracts a java source file from a tar file and then compiles " +"it." +msgstr "" + +#: ../../src/topics/workflows.md:170 02e7e81cdf7e4226973f910cd57b8ccf +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 +#: 3a88d92f41aa4daaad4f4cc6829184b3 646367f222ea41e5987561941d17c4f9 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 aaba75eb272245db82d072fed97b311c +msgid "" +"[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" +"github.com/common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/" +"_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 f8a6e1af5f0349a5a384be0629c37ac8 +msgid "" +"Use a YAML or a JSON object in a separate file to describe the input of a " +"run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 c4f854c7a279404da3688bdf424c7c5e +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 d383ce45139944cb85768627965d9467 +msgid "" +"Next, create a sample Java file and add it to a tar file to use with the " +"command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 84293afa7a6c40f2af0b980c89581fc7 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 e66daf8af53849109936c36ca7d2b2c9 +msgid "" +"The `cwlVersion` field indicates the version of the CWL spec used by the " +"document. The `class` field indicates this document describes a workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 8fbfbb587b264dcf98a3cea16dd36ef3 +msgid "" +"The `inputs` section describes the inputs of the workflow. This is a list " +"of input parameters where each parameter consists of an identifier and a " +"data type. These parameters can be used as sources for input to specific " +"workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 5cdbc4771ea841b4960362b930de2af6 +msgid "" +"The `outputs` section describes the outputs of the workflow. This is a list " +"of output parameters where each parameter consists of an identifier and a " +"data type. The `outputSource` connects the output parameter `classfile` of " +"the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 2e8a41fe43984dc6b4cf430e1ff66b28 +msgid "" +"The `steps` section describes the actual steps of the workflow. In this " +"example, the first step extracts a file from a tar file, and the second step " +"compiles the file from the first step using the java compiler. Workflow " +"steps are not necessarily run in the order they are listed, instead the " +"order is determined by the dependencies between steps (using `source`). In " +"addition, workflow steps which do not depend on one another may run in " +"parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 78c20aa5a5724da6a4c908849c571334 +msgid "" +"The first step, `untar` runs `tar-param.cwl` (described previously in " +"[Parameter References](parameter-references.md)). This tool has two input " +"parameters, `tarfile` and `extractfile` and one output parameter " +"`extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 1606a2f059eb4b0c9e90f2f0cbbe779b +msgid "" +"The ``in`` section of the workflow step connects these two input parameters " +"to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using " +"`source`. This means that when the workflow step is executed, the values " +"assigned to `tarball` and `name_of_file_to_extract` will be used for the " +"parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 b456b11e2760479bbf81a773a3e1f8ee +msgid "" +"The `out` section of the workflow step lists the output parameters that are " +"expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 0fa01fcec32049c989ad1d68841c74de +msgid "" +"The second step `compile` depends on the results from the first step by " +"connecting the input parameter `src` to the output parameter of `untar` " +"using `untar/extracted_file`. It runs `arguments.cwl` (described previously " +"in [Additional Arguments and Parameters](additional-arguments-and-parameters." +"md)). The output of this step `classfile` is connected to the `outputs` " +"section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 2bc9829f95584a269eb577c610b2a80c +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 0e5e6445bfcb42a4bd03612316dd7225 +msgid "" +"Workflows are ways to combine multiple tools to perform a larger operations. " +"We can also think of a workflow as being a tool itself; a CWL workflow can " +"be used as a step in another CWL workflow, if the workflow engine supports " +"the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 0b83c1028b0e43ba972609e4302bc8a2 +msgid "" +"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " +"workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 cbe1ef068b0c417b953655e132333447 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 a691c36a15044b11a6d037d16f818a6d +msgid "" +"This two-step workflow starts with the `create-tar` step which is connected " +"to the `compile` step in orange; `compile` is another workflow, diagrammed " +"on the right. In purple we see the fixed string `\"Hello.java\"` being " +"supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 2e9797fcd4f04f56b5d2b2f1a3e306d5 +msgid "" +"\"Visualization \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 28f4139911b44eeeb7afd31e9f7cae7b +msgid "" +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " +"CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped " +"to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 4a6cb397a20241beab24d956920a8379 +msgid "" +"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " +"running it we had to provide a job file to denote the tar file and `*.java` " +"filename. This is generally best-practice, as it means it can be reused in " +"multiple parent workflows, or even in multiple steps within the same " +"workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 dccb5472a5dc42b7946dd9245a71ecf0 +msgid "" +"Here we use `default:` to hard-code `\"Hello.java\"` as the " +"`name_of_file_to_extract` input, however our workflow also requires a tar " +"file at `tarball`, which we will prepare in the `create-tar` step. At this " +"point it is probably a good idea to refactor `1st-workflow.cwl` to have more " +"specific input/output names, as those also appear in its usage as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 de1e18b69f654cabb75e52b47058030a +msgid "" +"It is also possible to do a less generic approach and avoid external " +"dependencies in the job file. So in this workflow we can generate a hard-" +"coded `Hello.java` file using the previously mentioned " +"`InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 b947e62f4b3b4c10b95737f1839bcc5a +msgid "" +"In this case our step can assume `Hello.java` rather than be parameterized, " +"so we can use hardcoded values `hello.tar` and `Hello.java` in a " +"`baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 2ed0258a3a104ed5ba3b6b95ad998839 +msgid "" +"Did you notice that we didn't split out the `tar --create` tool to a " +"separate file, but rather embedded it within the CWL Workflow file? This is " +"generally not best practice, as the tool then can't be reused. The reason " +"for doing it in this case is because the command line is hard-coded with " +"filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 6584c0995288450b8a01c35fa231afb6 +msgid "" +"In this example we had to prepare a tar file outside, but only because our " +"inner workflow was designed to take that as an input. A better refactoring " +"of the inner workflow would be to take a list of Java files to compile, " +"which would simplify its usage as a tool step in other workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 19237513fd134c33801a7af08f74e70c +msgid "" +"Nested workflows can be a powerful feature to generate higher-level " +"functional and reusable workflow units - but just like for creating a CWL " +"Tool description, care must be taken to improve its usability in multiple " +"workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 b66e0d0a36994b3182a3784bda8ffc19 +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 3bfb9851302248568bb4535ddc87a27f +msgid "" +"Now that we know how to write workflows, we can start utilizing the " +"`ScatterFeatureRequirement`. This feature tells the runner that you wish to " +"run a tool or workflow multiple times over a list of inputs. The workflow " +"then takes the input(s) as an array and will run the specified step(s) on " +"each element of the array as if it were a single input. This allows you to " +"run the same workflow on multiple inputs without having to generate many " +"different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 78a5a600f8cc49ce8055c77a596ad833 +msgid "" +"The most common reason a new user might want to use scatter is to perform " +"the same analysis on different samples. Let's start with a simple workflow " +"that calls our first example (`hello_world.cwl`) and takes an array of " +"strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 f9618882e0a14a0b84ff9751346dc291 +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 4fe03daddd304a9b828fdd1c29f0d072 +msgid "" +"Aside from the `requirements` section including `ScatterFeatureRequirement`, " +"what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 7ab022708a9642ab8aa2e79ea7810381 +msgid "" +"First of all, notice that the main workflow level input here requires an " +"array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 fe144641fc8040b283f15b2b99ecb5a2 +msgid "" +"Here we've added a new field to the step `echo` called `scatter`. This field " +"tells the runner that we'd like to scatter over this input for this " +"particular step. Note that the input name listed after scatter is the one of " +"the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 f13d1b071a7f4a75a4cdee40ecef14fa +msgid "" +"For our first scatter, it's as simple as that! Since our tool doesn't " +"collect any outputs, we still use `outputs: []` in our workflow, but if you " +"expect that the final output of your workflow will now have multiple outputs " +"to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 b0b2e63d2b8a4fd0983e976c16440da4 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 47ac993a90fe46ca92e97d6b67b3276b +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 f5b8681b3c3b4890a86d7b9fb812d958 +msgid "" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " +"calls the command `echo` on a message. If we invoke `cwltool scatter-" +"workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 74e70fec6d2447bbbd2a5bc8af1fa58c +msgid "" +"You can see that the workflow calls echo multiple times on each element of " +"our `message_array`. Ok, so how about if we want to scatter over two steps " +"in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 76fed9e7ad1d4792b7bb364bb684eeb2 +msgid "" +"Let's perform a simple echo like above, but capturing `stdout` by adding the " +"following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 bef387d9be1f4ca19a97023cfdd1c910 +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 eea1be83da574f39914566d835701b4a +msgid "" +"And add a second step that uses `wc` to count the characters in each file. " +"See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 2043f12eb2ce4424b133e0dc0b62aafc +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 87ba95507fc44dbca4cb6c5283ce50f9 +msgid "" +"Now, how do we incorporate scatter? Remember the scatter field is under each " +"step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 e6e1a79638d74547b00c64e3c8b05710 +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 03fb16e74bf14c49b43e35ef6cb45030 +msgid "" +"Here we have placed the scatter field under each step. This is fine for this " +"example since it runs quickly, but if you're running many samples for a more " +"complex workflow, you may wish to consider an alternative. Here we are " +"running scatter on each step independently, but since the second step is not " +"dependent on the first step completing all languages, we aren't using the " +"scatter functionality efficiently. The second step expects an array as input " +"from the first step, so it will wait until everything in step one is " +"finished before doing anything. Pretend that `echo Hello World!` takes 1 " +"minute to perform, `wc -c` on the output takes 3 minutes and that `echo " +"Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 " +"minutes. Even though `echo Hello World!` could finish in 4 minutes, it will " +"actually finish in 8 minutes because the first step must wait on `echo Hallo " +"welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 eca3380c60094df2b91b44b5f7718fae +msgid "" +"Ok, so how do we scatter on steps that can proceed independent of other " +"samples? Remember from [Nested Workflows](#nested-workflows), that we can " +"make an entire workflow a single step in another workflow! Convert our two-" +"step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 6c61733fe4284f51a6b46e89cafe78c4 +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 0585f83162c349969391c9456a884f28 +msgid "" +"Now the scatter acts on a single step, but that step consists of two steps " +"so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 f209343966db4d46b4611d3620c3b496 +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 5a2661ce35dc4d79a15da1e17c0a95ec +msgid "" +"This workflow contains a conditional step and is executed based on the " +"input. This allows workflows to skip additional steps based on input " +"parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 8f7ee09c9d6b491195e2d80315dae398 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 966acff0d3d24104ae9673df8a790fb1 +msgid "" +"The first thing you'll notice is that this workflow is only compatible for " +"version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 d60e1df759654f1b873276cf0296f234 +msgid "" +"The first step of the workflow (step1) contains two input properties and " +"will execute foo.cwl when the conditions are met. The new property `when` is " +"where the condition validation takes place. In this case only when `in1` " +"from the workflow contains a value `< 1` this step will be executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 69aa8d3c9d9a4fe4a62875827648d95f +msgid "" +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " +"will pass the first conditional step and will therefore be executed and is " +"shown in the log by `INFO [step step1] start` whereas the second step is " +"skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 fee34c880e964e08b040adf2d3831803 +msgid "" +"When a value of 3 is given the first conditional step will not be executed " +"but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 cb9e82cf4b484ca7be19612b14fbdf33 +msgid "" +"If no conditions are met for example when using `--val 2` the workflow will " +"raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 8e7c3365f0f94038930f71666f05170f +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 cbe6f35c21044054a010767f2f0cae46 +msgid "" +"[YAML][yaml] is a file format designed to be readable by both computers and " +"humans. This guide introduces the features of YAML that are relevant when " +"writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 2cc21093311548cd837aa7b3f0939093 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 6e7ea76e8aeb477cbb8197efed33e53d +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 482e121a6e74428dbe6ad1f772f14684 +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 179290eee12343dd9aa4d49207cf7c68 +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 7880db40e98e4aaabdc96def3d9f515d +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 75f3b499494b445f9f9a532d178cbc10 +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 2b900b2779c84de5bbd3c933c56e5922 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 189db6d0e54a400eb5615e259354827e +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 e689c0e1dcd645348ceed51e91eb9ad0 +msgid "" +"Fundamentally, a file written in YAML consists of a set of _key-value " +"pairs_. Each pair is written as `key: value`, where whitespace after the `:` " +"is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have special " +"meaning in the CWL specification and underscored key names otherwise. For " +"example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 9532ac8e1dda479e890bf970323a0a32 +msgid "" +"The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " +"and `home` - with their four respective values. Values can be character " +"strings, numeric (integer, floating point, or scientific representation), " +"Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 91a057a7d10f438fad10338dd44c013c +msgid "" +"Values may be wrapped in quotation marks, but be aware that this may change " +"the way that they are interpreted i.e. `\"1234\"` will be treated as a " +"character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a " +"command: in CWL all parts of `baseCommand` must be strings so, if you want " +"to specify a fixed numeric value to a command, make sure that you wrap that " +"numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 d18c1f5ef55d4bb6b8334438fcbc96b8 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 dc6869049fc143b4af91d172a419a125 +msgid "" +"You may use `#` to add comments to your CWL and parameter files. Any " +"characters to the right of ` #` will be ignored by the program interpreting " +"the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 c3c7f5ecfedb4884ad5e91bb79ba2a7c +msgid "" +"If there is anything on the line before the comment, be sure to add at least " +"one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 84f16419237a4789ac0f3c682b3a11ee +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 269ca8e05ce14e899fc8b2a00b1e458e +msgid "" +"When describing a tool or workflow with CWL, it is usually necessary to " +"construct more complex, nested representations. Referred to as _maps_, these " +"hierarchical structures are described in YAML by providing additional key-" +"value pairs as the value of any key. These pairs (sometimes referred to as " +"\"children\") are written on new lines under the key to which they belong " +"(the \"parent\"), and should be indented with two spaces (⇥tab characters " +"are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 ce790af50da540eb9108ad89eae037cf +msgid "" +"The YAML above illustrates how to build up complex nested object " +"descriptions relatively quickly. The `inputs` map contains a single key, " +"`example_flag`, which itself contains two keys, `type` and `inputBinding`, " +"while one of these children, `inputBinding`, contains a further two key-" +"value pairs (`position` and `prefix`). See the [Arrays](#arrays) section " +"below for more information about providing multiple values/key-value pairs " +"for a single key. For comparison with the example YAML above, here is a " +"graphical representation of the `inputs` object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 c3c9ef616b5d472a894ad6330267bcd2 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 b8a7360f6e0640aa9a2c4907c1ba3fe8 +msgid "" +"In certain circumstances, it is necessary to provide multiple values or " +"objects for a single key. As we've already seen in the [Maps](#maps) section " +"above, more than one key-value pair can be mapped to a single key. However, " +"it is also possible to define multiple values for a key without having to " +"provide a unique key for each value. We can achieve this with an _array_, " +"where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 363da878600a4d229efe0ba79835d73c +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 209dfb0d0a1148ed962dbb33890a3160 +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 cd3a174dae334d0d977a3234e258bd25 +msgid "" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " +"can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 b0f0b10de8f54e1e951e480f696976f1 +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 b5597e8984ad4e0bad33433c1dab89bd +msgid "" +"Native JSON can be useful in indicating where a field is intentionally left " +"empty (such as `[]` for an empty array), as well as where it makes more " +"sense for the values to be located on the same line (For example, when " +"providing option flags and their values in a shell command). However, as the " +"second example above shows, it can severely affect the readability of a YAML " +"file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 5ad7d551d3d347a097508a8488f9d15c +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 58f80e6944f9402a810b9b02ba3ad917 +msgid "" +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " +"while we wrote this guide, though it also covers features that are not valid " +"in CWL." +msgstr "" + +#: ../../src/tutorials.md:1 8fdcc745f4684fa7816c62782507438e +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 3c933ac074ee4d94b7aeacb7abeaf388 +msgid "" +"This is a list of tutorials provided by the CWL community. Use the `Edit " +"this page` link in the menu if you would like to add another tutorial to the " +"list." +msgstr "" + +#: ../../src/tutorials.md:7 1d6cdf13aa834cb4a682553227d9f725 +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 606cc939c5014e2abdab163e4d726f1b +msgid "" +"[Introduction to Workflows with Common Workflow Language: For Contributors.]" +"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 3505468d39c34a20bc55f431a3c697f7 +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 e5731a11b89e492d8d751100a46c5226 +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 cdfeabb88f6245d9a687197d242ed3f9 +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 997679b781a84add9b6d8b1900deec35 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" diff --git a/locales/sphinx.pot b/locales/sphinx.pot new file mode 100644 index 00000000..e7779e0d --- /dev/null +++ b/locales/sphinx.pot @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 +#: d65b012160e9455eb4d2628279fffc42 +msgid "Main navigation" +msgstr "" + +#: ../../src/_templates/sidebar-nav-bs.html:3 +#: 4b3441eb77f448daa60718b7bfa862db +msgid "Section Navigation" +msgstr "" diff --git a/locales/user_guide.pot b/locales/user_guide.pot new file mode 100644 index 00000000..0a669946 --- /dev/null +++ b/locales/user_guide.pot @@ -0,0 +1,3122 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../LICENSE.md:2 +#: 4e203044f0464fd5a3256430391dde12 +msgid "Licenses" +msgstr "" + +#: ../../LICENSE.md:4 +#: 79a9837f877147fa8e3931968aae7fb5 +msgid "Instructional Material" +msgstr "" + +#: ../../LICENSE.md:6 +#: 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +msgstr "" + +#: ../../LICENSE.md:12 +#: 98f18f72afa043f9a79aa9b5fc8bdf22 +msgid "You are free:" +msgstr "" + +#: ../../LICENSE.md:14 +#: 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" + +#: ../../LICENSE.md:15 +#: 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "" + +#: ../../LICENSE.md:17 +#: b746b1e4dca14de1a8e18036b7602a73 +msgid "for any purpose, even commercially." +msgstr "" + +#: ../../LICENSE.md:19 +#: 6021e65292a149d5b15e14491f3eb05e +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +msgstr "" + +#: ../../LICENSE.md:24 +#: 8fb7a2946c384364814c6ec3910997d3 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +msgstr "" + +#: ../../LICENSE.md:32 +#: 8161753b7526445db319210044566200 +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +msgstr "" + +#: ../../LICENSE.md:36 +#: 15314ba527864eaa834cf1185cfcc4e3 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +msgstr "" + +#: ../../LICENSE.md:39 +#: b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +msgstr "" + +#: ../../LICENSE.md:44 +#: a091addc2dea4830a06bb72ead56c5ea +msgid "Software" +msgstr "" + +#: ../../LICENSE.md:46 +#: 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" + +#: ../../LICENSE.md:51 +#: 0f68eafafaef4b54accba7e13bfaa702 +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:1 +#: ../../src/_includes/what-is-cwl.md:2 +#: eab02dc13915490bb3c9ba744d78b6a7 +#: d4f35995b0f6494d9771a4be0a82538f +#: d6ccd4b546254f56a597d67dd4fdc5d6 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/episodes.md:5 +#: ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc +#: 436cfca6f857469bbff7c652df32160f +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 +#: cc11f5d29206492d9f2f0922882b6159 +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +msgstr "" + +#: ../../src/faq.md:1 +#: e2ed894d325a4f50a5e2dc69da5531a1 +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 +#: 61edb787dab04ca2ad3ed07616d878a0 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 +#: d5321589e7ed4f0db3c630cc39800791 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 +#: fc62427c0a004810b055dee90ec5e2d9 +msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 +#: 1c6b8a4194a14611b4061b1540c3807f +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 +#: bc7ad10c929848a3a9a240a3c501d299 +msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 +#: 7225a993d281421b95c8e3df2846a0e3 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 +#: 7ef1dbb81993473f948d9c6f3c64b381 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 +#: 450edf800a18423195bea4fe8793a2cb +msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 +#: 1a8cc75ea6174b9297871b2e58971077 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 +#: a7d84f740a714ec588503ee084fbbc34 +msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +msgstr "" + +#: ../../src/faq.md:97 +#: 569d553abe85450c9d1c37456bf412f4 +msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +msgstr "" + +#: ../../src/faq.md:104 +#: 95f5dbbd21084a318413b9528fb867be +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 +#: 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 +#: 8d86baa239364f799d4f9d5ea2b0e314 +msgid "The second method involves including an input of `type: File` in the script itself:" +msgstr "" + +#: ../../src/faq.md:135 +#: f2c109998c76434893ff16b17fdb2bd0 +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 +#: c2c752b86bf94d6fb3751f4dd81bc7a7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 +#: 2c38cc58cbb340bc935a5f00e96ba95c +msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 +#: ce6db54bd0f54839a5beb948530a21f0 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 +#: d06cbf89028b4638ad54c2529bcbfa25 +msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 +#: d53fb28dcad04e7788cba9e280a2343c +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 +#: d9e30e11533b4d53a144f5df7041268d +msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 +#: 941077158ec54ae19bfa2e2ad6662da1 +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 +#: 937cb94a370640c788fbc3fe0b19f2e5 +msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 +#: a1d57e15656548128a76a8b975c564c9 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 +#: c8c235a9bf6240628f0b5493ffebf7e0 +msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +msgstr "" + +#: ../../src/faq.md:229 +#: 3da4dcb043eb4423a53a14182949d9cd +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 +#: 89b90d3bf1ea4ebd88482d435241fac5 +msgid "To make an input parameter optional, add a question mark to the type declaration." +msgstr "" + +#: ../../src/faq.md:247 +#: a854006054ce4ffe94bbfa73bdbecbf2 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 +#: f80eb714e9df417fbba555b5dd5f4d8c +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 +#: 10af80fa13af4158aec7060550485350 +msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +msgstr "" + +#: ../../src/faq.md:267 +#: ad1c26711ccd4efd8fdb25f9293d33fd +msgid "" +msgstr "" + +#: ../../src/faq.md:268 +#: 49e2095b51f84f609f5d4bc088ad9745 +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 +#: 52b8538177c64090af51f5f6a696c28c +msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 +#: f96c9257e3734b8aa0cc5e065f74f944 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 +#: 7dc0540508084a3495ff3b2ac90fd323 +msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 +#: b53dc77466b24a67b52b8aadf4fab724 +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 +#: cf4e7f3977ae4f9b877072c2b1c4b533 +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 +#: 99b37739ef18443ca7c0e715a131e0c7 +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 +#: 9b00b5a55ee941e1adbfe89e133791e3 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 +#: 07922147f7ab487ba2a1e7c43c9f410c +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 +#: 7a11806f0c7045b48fe58a271f814797 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 +#: fdaec25650ab4b0fb1c527610e24ae5a +msgid "For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "" + +#: ../../src/faq.md:371 +#: 182959fc9f4746d082994e07d05c8cde +msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 +#: cc7752e9989e4a6d957682f479d6fc60 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 +#: 6db1ebd2d6c74ceca889662cd7df5cd5 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 +#: 3de2513c7d7b4569ba63f7e6d29137b7 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 +#: ae3a9188706649e28f97bc4ec34c0821 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 +#: e1ac97ab6ad3449b8c54933d25257f73 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 +#: f6c402f7f6974edbbb5582c8e22f3869 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 +#: 190099a242a645c9b9f8bc3ce89d920d +msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 +#: 06a4f6ffc2da4d43b453d4784b42efd3 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 +#: 1901c34201054a9cae199b0dbb8b945e +msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +msgstr "" + +#: ../../src/faq.md:450 +#: 2d498470524d47f18f9936ace6acebb0 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 +#: d7b044f5224a48eda09bc949cf645193 +msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + +#: ../../src/index.md:1 +#: 2754519265eb426b940bbbd2b8d64e1e +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 +#: f8d6e4cd54cb42c88182a43171d97bab +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 +#: 132d40fee3b84469afa80d5ff613bf77 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 +#: 0f47157605a34ea58770ea898deebae4 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 +#: 6d269e8d70184034bcb56385a6ca198f +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 +#: ed74c9a4b623464480e2c184668fcec0 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 +#: cfa67cf5521b414da6f7d34cbed283f7 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 +#: ee6b82bd86264e4bb1e8e4065b1e6b9c +msgid "Table of Contents" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:1 +#: e208c8a7506e41dcac9a403c5d2850c1 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 +#: ac62d326a68145b695e46b714d4e8156 +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 +#: 984e6676b9d04c7092bc492f195dfb91 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 +#: cbe1d761da5b403d9605fa1fb8e62fdf +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 +#: 3a71b269bd3c49eb913cf69b60373c24 +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 +#: b171b72c48d44050a3416a7a42c4021d +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 +#: b3df1607e9d242d78b22dc44335fbe2d +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 +#: 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 +#: c3869b4ec5ff47d99e8da79770722e04 +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 +#: 2482c84831fc4dfab629e7bfcfb41cbf +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: a5ebc727fb3443f78e81d6b7ed5ac750 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 86e6a06992dc4228bfda7add48e28ca3 +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 8c9772f96caf4169924d22eb929a4f0f +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 4fac209a62114798b79e4810f7a0148b +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: b97ba368fd664caab0494e2392795697 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 903a6796e3304a19ad885b2428b0e80f +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 6e352ac1f8e144c392ac5adf18c28298 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: cf2922f645904ac7955428ecddc37b8a +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 5f47aae608c041aeb4134d59dad314d2 +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: f6f589481d0c4891beaccb63160619ef +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: 4ace6b92f4e04a07aa202840ebe36417 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: 2d9f53b6ed5041dbb6c0b54835897856 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 907674a4ecff4826a2b880e28fc38f33 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 037cd0e5ceda482eaeaca03d51745aee +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: e4643938445b48cc80eb8973ceeb126e +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: c4c3315c96714e81b364f8cc003b87e6 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 3eb6a013a2a4478ca2ad134661f65c58 +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 074af9633627470485e5225326d5f20a +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 847951c055b94a83b1e081594cef22ee +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 44bde1fae06b4678bcac4f3224601296 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 +#: 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf +#: 3439764fab0e49d2bcb7c9fbae556e65 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 9d5100c7d0a040aea1020bf633ad17de +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 36eb4b3b966640af90faa55db3789cb6 +msgid "The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 2ccb956baa6b4376a04ad9fcc4654631 +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: 72889b830c514afe9a7cb1e64b5666a0 +msgid "The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: e29bd7f973544600be589c3b3f84cf63 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: c377a7f5dbe645cebbb6c7eccf831a0b +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 +#: 1769a0cbf4de4d77879c1f202cd11af9 +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 +#: 950370f0a36048b38e1bde9b78f80816 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 +#: f01faaf1b253407cbbc2f353c24774f3 +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 +#: 353b14f06ee845d0a06a829643e31534 +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 +#: b5a0607096814c0aa577f977c3b57c54 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 +#: ff2bb4c6504b456bac7ca9c514414dbf +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 +#: cbbcce4c2a96471b8b0ae3593ad59de4 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 +#: 5089fdba8aed4113983fa86e698df98b +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 +#: dbaa4bae22fe4d05b18d7351967ddbc3 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 +#: c05187af85be41b782678b79627f8fbf +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 +#: beb6cf4d7c154eb9b6d7fe024a318ed7 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 +#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 +#: 56d78c95daa54135b6aa9b2bfdc34d01 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 +#: 0f2704bf1f7148be95e999e312899f11 +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 +#: 86264c9e56104ecea9146407c379aae2 +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 +#: 0a0f0e5151ab4c498b4f8a12c016f28d +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 +#: f7aaafeee230400da056464c853582c2 +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 +#: 5eced7e4cd084e8a806b1d3b12d0c000 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 +#: 040c019b6e844eda8c8c2b210852516b +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 +#: 6391e08e0bde49f4b21286d8fdb97433 +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 +#: cdef47fca304479c9a9df75afc0afb35 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 +#: d41c4bc740aa474ea09a7cbd267c8840 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 +#: 24d7be55d3994f0b82c38da47918e0c9 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 +#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 +#: 096d0a50f69e48bd9915238d1b4264c1 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 +#: f9df974a8e2645a6918e67466bd1fdc2 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 +#: 71ebe91d4bda473abe87578929433212 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 +#: 746c6fc9c29d466494458a08d4c96672 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 +#: b9cc5a843a0f49daad56e9303657bdd5 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 +#: 34ab40437ab646488ba3ee86cd7fe071 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 +#: 705807fae182425dbf4244dbf2be1226 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 +#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 +#: 164c438baab54ec19bbb4584a10dd411 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 +#: bf8be77af6154326b28442c5d2e2b852 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 +#: 695184d1b45a42f393e2da99c3721773 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 +#: 7c4f45b3e7b549e186126693aa4a3d4f +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 +#: 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 +#: eec6c07455384630809ff1c532bfe7d4 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 +#: f6b39b12bd5c495cb53e2795bf9200ed +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 +#: 2fdb62a13f9447bc89183426260ce781 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 +#: 1f07135156254f74a6b043bf33d00cc3 +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 +#: de344f356b1c466d9131cdbd4d7353a3 +msgid "cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 +#: 3f9324ede11441f58d93875867034cf0 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 +#: 6ce8b81560e341c580d316d69202b268 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 +#: 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 +#: 8a9a50b0ebe847ce90593881ffe0d69c +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 +#: 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 +#: 9390b03889de44638141d705e0ef8322 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 +#: 12042e411482458f8c35a2491f9433e0 +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 +#: cdd4196f9aa34beba115901ec97913b6 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 +#: c43d9675ed134b78b02acb5a102a764a +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 +#: 280936bb2a22469799b2c9e9ba22adee +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 +#: cb203354977d42a58112d09357f62565 +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 +#: 9e51962a7e5c47248f3e20703ae101eb +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 +#: 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 +#: 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 +#: 498a43362a4749f3b8b433709d34a1d5 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 +#: f3e56aedd56b4b93bdc3894273e8c144 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 +#: 81481f5b82e4488398f87f0a169bd359 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 +#: a81342e756d24c40acc15835d0a768f2 +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 +#: c12cf89f8b9a421ebd05330326e219b3 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 +#: 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 +#: ce04027dfcfe4b7b91ea3c2136b18b23 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 +#: 0d8a788402914ebd8f09a5ca80650011 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 +#: 6d0b679efab24813a7a3b709ade940d1 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 +#: 2ea056ab04b6419a9faf350de22a17f2 +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 +#: 1a44a545434b448aa956005deeed90a8 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 +#: e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 +#: d4cdbe870a6f4a68b542ca719d989062 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 +#: b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 +#: 5535b98e8b1342f09f003ec6db2b44b1 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 +#: 77e43c7117fd4c52b140f0dd52cc3963 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 +#: 7282abfa7155497ca47c30f9abfb6474 +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 +#: 176d8d47830f4031bb95dc231ebf1303 +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 +#: 82a7ca3703bc4f0daa18942a1ac8943b +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 +#: d039a9d6461c44628d4660c00d9ce6ff +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 +#: fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" + +#: ../../src/setup.md:9 +#: 1330bd38c4b5495f890b98c669f81a9d +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 9c87c76c690948ac8e18088a0fffe679 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: ad00d94d4fb64bbdac356e64dd3803b9 +msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: d8110ed19da94ad8a9f56e7006c4a2cf +msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: a74935dc31664e979ca8f90a6a4ba53c +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 +#: 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 6359191b4f684d5aa3602e4aaf394883 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 9643449da1da46d7861866dce490cbcb +msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 713666580a0a4466b4ba6e3eb2b54f0a +msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: d50574c8b9694f83aa376d39b9a6fcd6 +msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 +#: 612c4a66c36a43d4ac5d74c1757d6845 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 +#: 939cd9e9eaff4e3ab74fe707a5d4eb21 +msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 +#: 4bcb84707acb40a0bfe2ea0853cb10b7 +msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 +#: 4dee8504a8e5496081dadc386ab45540 +msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 +#: 674c238b25e240eda05e22e399f2f78f +msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 +#: b651f80f47b4442fbf29454a233697fc +msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 +#: 263a127a77cf4c41af76854f22f1f260 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 +#: 3a87a0fb2a364e3da5aaa4017e430b19 +msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 +#: ecf2b9c0b1664afe9c4e180610610021 +msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 +#: e24cb13d98014e558b6a6946758359e0 +msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 +#: f2b14a92374e449d9fb1e8c86ae0dd61 +msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 +#: 928e3df7ca3e479ca6474a8e72cf36eb +msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 +#: d355f035676446c88b028f327aeb4829 +msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 +#: 339b852df24242189d6efcd2898a3396 +msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types/\" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 +#: 3ef57e6862f240bebcf193a52397af0a +msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 +#: f1a7c4f896a04a80b0c5f6a1db61ff8c +msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 +#: 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "Custom types should be defined with one external YAML per type definition for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 +#: c858f64e66f048a5b0032ef3e4d83694 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 +#: fae385da16aa443da996fa23ac03d6ae +msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 +#: 92430be71ecc40e18bbbb80d5576c613 +msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 +#: 387d83db81024f65aa9a890c2d07874a +msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 +#: d8e2280a75a74916a1630afaa2fe2ae3 +msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 +#: f1c1340f9745458980e0fbd641738687 +msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 +#: 5424e5472c3d466fa2a3d2022c6cb475 +msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 +#: 3f4e98f6bfa141feba8c4b120e3d03e8 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 +#: 12f57b2ba76b492abe1816e06bfb1417 +msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 +#: e1f657a46ce94a0d83671540e2cc2dab +msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 +#: abb83f0097654a43bd78639d3dbb2bc8 +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 +#: 3b1a9ae3412f4d6e96a39b9a16934232 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 +#: a5eacdbc9aa142c890b177869da4143d +msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 +#: 1849b8f3ae1c4a84ae59a78ffd6b371e +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 +#: e3bdaceae8784ab0807b2cf356a98580 +msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 +#: ed521ac365db4a6ba5a1051fbaa2932e +msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 0cf51b6da6884065ae42032abc20eb0d +msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2df3a3a9094d4b79b1d5dd99195f3bff +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d3f74c3b094a427fbec831afab657d50 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: cfffc518ba6e4ed1a80762ed6f7d25df +msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 9454a330b9324744b89448f2694b1b03 +msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 7f8d99a30b644457a62ac1523d0c72aa +msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 +#: ../../src/topics/outputs.md:77 +#: 2d2ef4769b2347e79db827655f1bcdeb +#: 2699fbc4376148af91b7a5a6cdac467c +#: ca03defa3ad14cf698171cb09e3055c1 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 10d1373bb14a4a3cacd3b92a2f83382d +msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 70e257091bdb456e8957f90a8fa90e8c +msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 1741804e33aa43ce88b4320c11ae5973 +msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 +#: ../../src/topics/workflows.md:198 +#: b372f33c65bb4707b2a462a960bb1373 +#: 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 +#: d6255506eebe44be94c5ce703c44a513 +#: 7bbd2d738fc54649aeb10f8d2bc38b6f +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 +#: cb34fd4c8cb04053ada491a227651048 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 +#: 67573252cc064b27ab13eebc468ac58a +msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 +#: 73e68b3af9cf41338d843c0c40e50cdc +msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 +#: ef5f35acb97f4ddfad7b688712f53484 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 +#: 7015dfa99a6f4cfb87ebf0ed61e8043c +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 +#: a999b1acda2641598086648c64aa3831 +msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 +#: f8c12a58cb0b46a488823c6ae95f25ea +msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 +#: f25a63e0926d4932bbe64b2e4bdabf9e +msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 +#: b0a4df0fd3ca42338cff4689235dcf4e +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 +#: fecfbb44456640d8ba05e519bf2ff564 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 +#: d718630a296545f3a989c8c71e9ddc77 +msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 +#: 9a97acd430064710bcdf76edbd9f711c +msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 +#: 59014808cbef4c02aaef03129d8a29b0 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 +#: 3c821c9c46d841ec89b8a5b1018f3af8 +msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 +#: bfdebb32440a4034beb42135e38884e8 +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 +#: 777d4a52f7554eff84db2df6d4d0f729 +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 +#: 48deb71f361a43e48a56ed483075bca8 +msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 +#: 716b56506ca7470299899c5d820a9ea2 +msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 +#: b63e6f5a2e89431c8fc7d04f47fd69fe +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 +#: 39727e9058f24b62b8746a46d3f812c2 +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 +#: e3ecac0a8e604f2b98a2a12b0579990a +msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 +#: c8d648b765ec499a8e9c464590838492 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 +#: 007a345b4bad49cf996c4301b8386473 +msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 +#: 2edbd398eadb458b8eacd5fa5496f0a2 +msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 +#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 +#: efb5fd14988c4e2a8f834ee5369d4102 +msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 +#: e833649b951841c49397796f996d29f3 +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 +#: 276f688ba7cc471a842f085ca852b1d9 +msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 +#: ebf399ea4d5f47b9be03e24f04c69f2d +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 +#: 65e0cdd505b944caa40f65e612cdddfc +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 +#: 8b70a1ad70514039b97164fa630c12e4 +msgid "Note that requirements can be provided with the map syntax, as in the example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 +#: 2f28ab412d2843ffa5f14acdc01fc732 +msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 +#: d957f55a6377422c9834f85d45e35009 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 +#: cbec9277b5004e50af2728cbda0df740 +msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 +#: e259f55f8000479bbd8009e25cf0ca6c +msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 +#: 1acb064f7a4a482aa0174bdc847c6382 +#: 0222780b98ac48e89b1b4f57c9df8590 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 +#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 +#: ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 +#: 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: e4e68011dc5f42e4918c747afa7d764b +#: d44e3cfa661840eb851782e24caf1b68 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 +#: 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 +#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 +#: 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 +#: 8210b36347a749889450529ecdf4ff0e +msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 +#: ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 +#: ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 +#: d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 +#: 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 +#: b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb +#: bd61499b71e64164878dea08d6d7141e +#: ed875a006df64f9e8a55fa5e9fa87404 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 +#: ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 +#: ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 +#: 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 +#: 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 +#: bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c +#: cd7a0190511d4613b09600a3b1e9d55f +#: 47def3b078e2402182039be0227090ae +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 +#: 23088850ad02459696f6bbd385109aac +msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 +#: f02257a822ad46ac93c5981531cc85d5 +msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 +#: 989a1c4aaa1143be9f53b90cd8b6d500 +msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 +#: 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 +#: d555a3d991e344a5a8e1289168d7c6d1 +#: 44b3f123c9b04a308c1161b742a7b34b +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 +#: e9fa9430535c424fa3e8be5d460d2ba4 +#: 0e306cc923974d1db83fdfb45105a11c +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 +#: d289541e460147aa933f7878996f8649 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 +#: b0290d1a477b48119e17cf1fed9d6dff +#: 446f1190af7a40a0913ff04ce7aa938c +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 +#: 81b4d1f23a3642bfa9bb395b94260cd1 +msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 +#: e1cde4aa32c041238ed2596173c6d824 +#: 557694f82e314baa9ccafba14d6ff2c9 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 +#: c2a92d3eca7f4ee39cec649170eeea53 +#: 3c939769ede94602a67fc50c435741cf +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 +#: f495da32f05a4a5ba9539be0a54c1a59 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 +#: bdb4c68a175047ddbe141ca24960127f +msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 +#: 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 +#: 718ceee9973240ec9c100977bbcc8921 +#: 2b25152f6df5494a8632f3ce631c20d8 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 +#: c07ab08eb75d4528949c56a3d7c12b28 +#: 846cd427ae25410eae7c920b237edcb0 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 +#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 +#: 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 +#: 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 +#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 1f39f016524a459895ed03c72d74932b +#: e3b76f42c924489f9a0bcf5a7b636d23 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 +#: 97b61352363f47cb890e8937c5613fa3 +msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 9359ef94c41249ea8e76fe629926054e +#: a258554d462f4f5f83ece28d5b2fc584 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 +#: 8d0b142bb7ed4e61b8fb03de197240ce +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: effc0208cf4f4551958db6e526c0528b +#: 9d4889c8cec24351a7a9e3c547e331b6 +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: be6c1e85c7b6495d8086c262daad20e7 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 2183ac54ae10428388649daa57b6a7f4 +#: 6abeba392b0444b19f92a19f178a4682 +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 +#: 0bc424ef2ca346099f29b937379908a0 +msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 107b54b832df4d408d1315bdba05b4dd +#: 949c376120d8441796ec9c89364f8851 +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 +#: 10d36a1adfd04144b401c993b12b4094 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 +#: 29b73e1dd72744f68377f0a38c10f062 +msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 +#: 38a2afaf4a6c4d04909af22c93f2808d +msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 +#: cd74f34b21af4de9be96fd897efc469b +msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 +#: f12e371f3f1a4b0cb2cff9800352d48c +msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 +#: 49d0fda2fc144e0b8b7c92afc1d8945e +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 +#: 8f0e8f050e334ac08334e9215e1dcf61 +msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 +#: 26c74b11bb1849cea0763bb74ec43e42 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 +#: 7a6be0005a6441feb67f036d005d7885 +msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 +#: ed590f9e6f4f425da886b110295c45db +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 +#: 093235307d6f47d4858e559b780ef5e5 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 +#: 06635145b441418aaae84dc804f3d6ac +msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 +#: 973a9b257b1a4f0dbd4444d4f11dadd7 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 +#: 04eaf1f7c630450db318dcd8b7626e15 +msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 +#: c4098489fbb049789f022cd3e5c3d49b +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 +#: 5979e4ae5c424276bdbc47f69b379d0f +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 +#: fd4579a3c9844492b314b5c3c1775fc7 +msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 +#: 3f038e7371f84ed9b4547358dfb55a11 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 +#: e024bcb70e04412e90e1838426d1b69a +msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 +#: a3db21c0b3114802a8a5b610e252ef13 +msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 +#: 0f5bc8520d6a4dafa37c65343da9702a +msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 +#: 5cb830da47464a8b9c3950983fa4d56f +msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 +#: 0535d5de416b4ea3b2f5996583deecc1 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: f558bcf2a993482195cd418b37761809 +#: fb47f73c38cf4ec59bd3021866a631f8 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 +#: 74b28c1b09c6429b82e462e4ec61808e +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 +#: a2ce43b391864e8bbde16328cc19b32b +msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 +#: aebee48b742c4145a600fd2daf8c75dc +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 +#: 56ee4dcfff6141d5bef80eb96559876d +msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 +#: 8d3a6d83e2e54c56995893c41590b7ff +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 +#: 5abcdebfa1cb401bb8892553be285fd3 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 +#: d3a55f71dc244026a97902de9ed819ea +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 +#: 96671c56523c4ea9992fb5dfcfa6490e +msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 +#: bcc6246742cb46bfb185e415c4a3431a +msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 +#: 86dce36de687449c88fb5eb9d64eb045 +msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 +#: cd9cea15f57b492ba4098237cd7c5bed +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 +#: 8bdb875b63104f699efe28ea0abb1e3d +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 +#: c6a0151a68494c0cb0176781e65e252e +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 +#: dc5e6b5e01d64226bd5dbbf3175fe010 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 +#: 36ab1d9edafc4831bb1bca5f123b04b0 +msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 +#: 7dc630ea86464b1dba3a4e5079260b3b +msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 +#: ae37901a8dbe48a59e27ab4e2e6e2d30 +msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 +#: 651e032007ea4a119d20c820bb61f86b +msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 +#: 0b056dde9e87428996e47870b12119da +msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 +#: 628124a1670b4b058bb0fb6e495a099c +msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 +#: 10ca6321ce3e4b08ab6a5bb380b19c11 +msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 +#: ec2adb3912bc46e28891229e9e0d9a1c +msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 +#: a519be60726a44af9941fdce04735353 +msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 +#: cb8fc8c4c79e467eac5fab4ca685201e +msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 +#: a26cc105716f47cb807174c9003153b0 +msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 +#: cc159dd5fe5748caac838862f5b8c4d1 +msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 +#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 +msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 +#: 6812698e9ad84d3385de5e88e9dde0b3 +msgid "The `baseCommand` field will always appear in the final command line before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 +#: 9654e65b1c0642dbb5d4f34edb211989 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 +#: d1f02be278754267893dfce5a940997d +msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 +#: 01f30e38dfdd452dba3a996073936e16 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 +#: 787d4bfb093c4ad287b902084706b751 +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 +#: ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 +#: 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 +#: 9db68837918a4a349f32f15f12697a1d +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 +#: 75d59e395c66416cae9b352db5081516 +msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 +#: 874c6f19abbf45d7ab7d30a378c4048d +msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 +#: 5d7d7a28cc5d4862803032aec78174d9 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 +#: dea0d4b681f94e73b13965dcfe75cf7d +msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 +#: ddf598abf4f34aca9fffa045860fbf96 +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 +#: d52a8089920e45bd89d582533b50e3a1 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 +#: 750474486a84482292eeba45f118287f +msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 +#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 +#: 1eb0e39bb6d04b8cab300f44a79f3add +msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 +#: bc21ee10bff843689cc98ac6630edcea +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 +#: 4b2ab812f62c4f949dd25c8527f2411c +msgid "In the third example, only `itemD` is provided, so it appears on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 +#: b771302d1bec4050a9417b080eef76c9 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 +#: 2c3b884cb1c54521900cc90782e8a58d +msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 +#: a1073b6306044dffb414319ae01f68bb +msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 +#: 4a31c733092142b1af834eab1747c224 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 +#: 9a1d92334685449386dfa3b3a899ed48 +msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 +#: fb623af4c480411b8fde28d01c981411 +msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 +#: e98e165f6bba40809c90473d72f9d592 +msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: d33aa2353ad44fb885d3a1ee48263dc4 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: cd64d2d828834cbbb24ea5358caf5405 +msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 80af387fe3ff4e2da999903385bd602b +msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: d402bf528c7f4eb69aaaa275be2bf1d4 +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 +msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 2dfbd4d580044ed083992f3ceb1bc64e +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 +#: 8acf361cf77c4d45ba3f2e344146259f +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 +#: 83d3b9a0ed3148fda9ce72cd108cb9e1 +msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 +#: 5565c1b2d8a349169a305a9b26b4574d +msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 +#: 49cf614893d8438299b3bca384eb40cf +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 +#: 88160cef4cfa4add9020aa89511a5749 +msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 +#: 2f73a786b5d94dc0b23ed0cdd185afc8 +msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 +#: 730ba1434a1445ae847ec6153b6a3b72 +msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 +#: 98d9b8d867594543890af99e77e24edb +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 +#: a25d0b1e13324b40a6b8fcd227948c4f +msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 +#: da077da5eb8a4ffebfde041fc16300de +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 +#: 1b3016f0462f42deb42ddaa33f28bf3d +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 +#: d661df070e3040869da412d07a71f716 +msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 +#: a11585474d3849cca5467512ed964743 +msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 +#: 2682f9ca8e604a0c9986f7746fdec960 +msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 +#: 7e3fa7baf0f549ec89457e7004ac9545 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 +#: 22447a560f6f4317bf67bd7c4336126c +msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 +#: f1ee2e00b0cc4112b51c9df3a919b73f +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 +#: ad8e1acb251246d2a47c39b20d4e483a +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 +#: dc200c6960ae4476a772645d021f14b8 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 +#: 52703d6b7f914097934bfad13663abeb +msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 +#: 5e1c79df657d4a6e84e055dd6b300a5d +msgid "The field `outputBinding` describes how to set the value of each output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 +#: 329d2809dfae4f90bc638f5f03a47ee3 +msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 +#: 96df2d45e42441d49ce193ccbfab78a3 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 +#: c6bcf7c6a8774dd6be41cc775848c3b8 +msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 +#: 9d86c03ab44841c785b924cc44727e31 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 +#: 2fb58c2feaa84970bb5274c49f4b5b64 +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 +#: 9647019d8c37466886e7aab6f176634d +msgid "You can also capture multiple output files into an array of files using `glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 +#: b9eaf21f5e014eefaae301c47dafd144 +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 +#: cffff6c43b4945daa3b2a49763bc50ae +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 +#: cc067051f22f433bbece08f60933e002 +msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 +#: a190a6440ec34898990cdac05d809f22 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 +#: dbfe2c1123144316aa026374b0f353d3 +msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 +#: 280f1a07d0ae41d7a4674504f832fcf0 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 +#: 5c64d938862747cb9fb52515a656ce27 +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 +#: 074cf5d912854d8c864607cc24b15302 +msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 +#: 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 +#: b54240bb94f746bba7511633aa969db0 +msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 +#: 8b70a072aa87414c88e89a3e19af0a51 +msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 +#: eea20f89c45f424a888178df53713b28 +msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 +#: cb4ea13f5db84c0da43df3f7f2478d78 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 +#: 6d3fb423e6c4434697cd113fb27e28ad +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 +#: 7647e0229a924f988cf02b7812a55c06 +msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 +#: 9d663249666045618a0d3acddb85a9a9 +msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 +#: 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 +#: dbf6153cd02542a6a01c172803122b7f +msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 +#: b6250cf6fa8a4a0c94b33302e0decca5 +msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 +#: fa6ca3bbc6784380a03a950a6f49a180 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 +#: b92b516e537a4773ad67b4af586e7a25 +msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 +#: 467a701228504d06b971b79a59c69064 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 +#: 2634f989eb304009a8568d70ed42786c +msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 5d8bed66282c408695292ea92a03b2c4 +msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: 958178d1fa8843aaa0541e2bb115cfd4 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 +msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: aac74f957774479a83aab4c6ff1390ae +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: b75d29d1d55d44488338f9689f156855 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 574d93d1d592458a985f259519c036cb +msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: 82e48b3e3c3f451480cc0b6a529271f6 +msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 02e40154eac74ecc98d0447d03475b44 +msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 8cb1c5d9b1a54c40924099494eb766c6 +msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 +#: b85eb83e05e845d7a179f1b1d74db444 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 +#: 35f97d37492b4c7ca3ad6cfc1e6fa366 +msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 +#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 +#: 0f7508ce59754a7eb230dea6042244c6 +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 +#: fbe0c65b444441f785d0054176d036a6 +msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 +#: 1b6b7a75cc754775bf9dd80c0941e8da +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 +#: 9a710602e00c4934ae3a3b471aa68458 +msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 +#: 21b5be7270a14f0987240c81d1ec879b +msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 +#: 0490b1fab86749e49b473949c52bbe8b +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 +#: cfe9d8241fe84bd5b74042a5625d933f +msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 +#: 764d933cc4da446abd8dd8f913f05dac +msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 +#: c93efc6d4e004859981ee7f5fa28ed03 +msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 +#: 546601da44cb49bd9611b1c85807fd90 +msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 +#: 7e0bf00f8ce542b9b009cdcf1945a9e5 +msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 +#: eff5f28ca83c458a9b07faf7a81f7e91 +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 +#: 2e634f3737d04d279ae78ceee4b0a664 +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 +#: e07f33d01b804663a25ffb08aad74821 +msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 +#: 7a644506619a4f08958ec7d4540cd557 +msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 +#: b5195b7d8eaa419fb2b90cb33a57783a +msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 +#: 7921a837ee744c5aa9a5bda04b0c8db1 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 +#: 387e9bc9381a4450af54aff77e4df6a2 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 +#: 2713594c937d4c528fc8d04d9e9819ed +msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 +#: cf94c1424fc2413c85647fd1ee73d951 +msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 +#: dc0452107c604e29bdf32bb289fe5db8 +msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 +#: 1a5596243cec4c948d9b6bf0bb12fad0 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 +#: 483181f498fc4d968b5fe6ef427709f7 +msgid "Notice the CWL runner has constructed a Docker command line to run the script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 +#: 7487485d6aa4458089a4b4bdf107ea64 +msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 +#: 7394e7690f934043af617436b40845f0 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 +#: b9ae9e9a896048caad7e6c38a5bc1bd1 +msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 +#: f228fb7953ea48ed99d89880205f4620 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 +#: 5870ac44e4c24b8daf5f06c49f95ce04 +msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 +#: a913c76d06164fa18718a8a6a7dcf0d6 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 +#: 93188ed43ee949cc98b3ea679ce14feb +msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 +#: 36618126a4df4326b236ebe2ea42cffa +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 +#: 1cc17ad26e9c474b895ba5cd20c8b66a +msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 +#: 24aca0bea4d94e3593b844cf0586cffe +msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 +#: 46cc4859856e4367a9e5e68eecd48b73 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 +#: 9c56528acd5f49deb139e034dfbfac7c +msgid "This workflow extracts a java source file from a tar file and then compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 +#: 55ab007d472f43388e4c77aae8f165e7 +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 +#: ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa +#: 307b6618a92948fca4203ccb497c77e6 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 +#: a2dd833fdca4443181648e41051a5232 +msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 +#: 7e40cc9f9e1341c195e843c009575b94 +msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 +#: 26c51dcb76364ed780376aecb7cbacda +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 +#: 6fcf8ad3d1bd49afa4a105622437bd59 +msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 +#: 71cb81fa4511495b80422244849979e4 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 +#: def35d6021394def80a53ae49a2cdbde +msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 +#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 +msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 +#: c84d4450bc6a475dbf34e0b22cea9130 +msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 +#: cca9665f6daa44b49233baf34ab9fcc7 +msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 +#: 547edbf5fa424b8286cc21674ff159b0 +msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 +#: 7ca248888b9d484cb544cd76ba538662 +msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 +#: ae6b240718104380b08db5552d7355ea +msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 +#: e5a8b7f84be64020b191099f3fad30ed +msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 +#: f0b04849253c4693904512ddd7f9ce84 +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 +#: 12a06d8358534102b202965d4258c18e +msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 +#: 1658cac0de1b47e9b60f6d4a4ad9bb19 +msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 +#: 49ed137fe996452a8534c68d100db941 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 +#: b7f93705e5b8416696be01850072e8c0 +msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 +#: e87045829b344089ab59dc27063ddd7a +msgid "\"Visualization \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 +#: 42ef2f145b824d69b63abc1da175c216 +msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 +#: c61cedf543664d388183e04b3939cc39 +msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 +#: 9e39e3f1501c4fcaab3e8962e090f6be +msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 +#: 03e2f767c4da461982fc3c0f3ba94762 +msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 +#: 3bea5822b8694e2aa32c446e1c54a045 +msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 +#: 426023bd6e3a471cbb30dbda3d6f9e57 +msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 +#: 0d498cd4caf54c15891ca1afe58e2727 +msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 +#: b2d75045e02741b4850f5ff1243f7858 +msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 +#: cfa765264a27411ab914de569aa3dac4 +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 +#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 +msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 +#: 5fa79c62049a447c8328ebf9db54ebf4 +msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 +#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 +#: 3a67d77a2e7b4c0bb61cc3585ceae942 +msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 +#: f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "First of all, notice that the main workflow level input here requires an array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 +#: d947c54933d64aad90df392a1cedd63f +msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 +#: 651d35997332404186aa6d5711da4a3d +msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 +#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 +#: 842b926ae34542cb9023021f137b08be +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 +#: b662c1a5a4424c8d8350a806356acc61 +msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 +#: 04d6babfd87343d7a5f13867ea02b65f +msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 +#: 2eaacf1a90204a2b9bd621344560f2a1 +msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 +#: 242993d42b164ee5abe7ca10d45856de +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 +#: 4a94e5f7e1bc4d628702140e4e51d6d3 +msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 +#: e61d93b848184c8e8e573928427b4d0a +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 +#: e3a7182f00f440b8b5461da91194a64b +msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 +#: 99fa96caacaa45cb97aded9a24fcac6d +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 +#: b5338f39e8c74ff28e139da68089a742 +msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 +#: f6d92156d67c4a339bcfd194cff897df +msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 +#: 1c9e386922324ec8a59306572c19fb8b +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 +#: d80ab383eec9402faba997b548fe42eb +msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 +#: f7d2827d97db4bf4ab84b5d6621c3b48 +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 +#: 49217c02f58c43ff9ec00f10da8d4e84 +msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 +#: 20b9f181420c401d8615c17a10027517 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 +#: 8dbd56473f8c40c0bb12a48be06117e3 +msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 +#: 78d7f3ede2c746d482042adef050b2c4 +msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 +#: cbbf93c70fe04ba7932ba25758ddc611 +msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 +#: cfa1c1fde4454df283f87cc54a9c59ec +msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 +#: 1a8be2950cbb475bbb2617e005f0fac9 +msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 +#: 5f09d4d897cf457d80b9a11b8c01747e +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 +#: 5d83c56102e141cc978500f678dd0c1c +msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 +#: c38438fbf9a04e729ec2e3c962435289 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 +#: fdb9cc750cec43ee962517e637dc5fea +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 +#: 08da9cd8056b4ddd8f5150cc85ba72ee +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 +#: b027fc234ed943bbb00d4c6bc03c040a +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 +#: b8befec0d8684638aaa616a659e0100c +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 +#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 +#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 +#: 98056c5cfd5640ad9de0679360797cc7 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 +#: cda73485875d4c8e9464679a20558616 +msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 +#: 98cae24919b74c088a5d89706aec581b +msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 +#: b4b0940b4b5743c09637b36b964202d0 +msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 +#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 +#: 9ca3554d771d45998e88aaede525b227 +msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 +#: 3fca839cede94cfd8e4f605c73ba699d +msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 +#: da34c635707345b2a5e85a2fcd30bbaf +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 +#: 3ded0f125249485c921994b6e6b93ac9 +msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 +#: 53ece35d309a4c8d99f1efb2122a7092 +msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 +#: d74321b111d84ae7a515f2f17dd39e23 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 +#: 7fc0bdf2489a44f2a29e71b86f7c0055 +msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 +#: fd64dd818ec64bb6aa9a11586a5747f6 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 +#: 8c06e542dd4144fa83388d8142552c8d +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 +#: 87bafb845c714b109874f6137b84462d +msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 +#: 5ab9ddf613a540a2b8228e37600cc5dc +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 +#: fcd05b1ef31a4046946a2399c7fc5575 +msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 +#: f4b8fc8236044fada420def13a02813d +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 +#: 859368c1f25c4a4aad57abfd046c63f5 +msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +msgstr "" + +#: ../../src/tutorials.md:1 +#: 2203c93f02ac4514a43508ecb98dfcc5 +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 +#: 5d92464923c245818c070fbef102be89 +msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +msgstr "" + +#: ../../src/tutorials.md:7 +#: 8a5cd557dab5456bb41cdc24af73b50c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 +#: 13d7e2e92e96432787c712cf6a595424 +msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 +#: 0abdd85c9b964a4e89ba3d80a6c78d6f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 +#: 3cbf1f69a5514fd3bee90e68b201190f +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 +#: 68c97a7065634d02956f3f5c1d4eeb9f +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 +#: a67c7e0eaf4e4d27b3e5db303333a088 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" diff --git a/setup.cfg b/setup.cfg index f4315385..7ccac7d0 100644 --- a/setup.cfg +++ b/setup.cfg @@ -40,6 +40,8 @@ install_requires = sphinx==5.* sphinx-reredirects==0.1.* sphinxcontrib-runcmd==0.2.* + python-Levenshtein + sphinx-intl [options.packages.find] include = cwl* diff --git a/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl b/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl old mode 100644 new mode 100755 index 3a2e4538..a6f7287c --- a/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl +++ b/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: Example trivial wrapper for Java 9 compiler hints: diff --git a/src/_includes/cwl/creating-files-at-runtime/createfile.cwl b/src/_includes/cwl/creating-files-at-runtime/createfile.cwl old mode 100644 new mode 100755 index 5e39a36f..d5694aab --- a/src/_includes/cwl/creating-files-at-runtime/createfile.cwl +++ b/src/_includes/cwl/creating-files-at-runtime/createfile.cwl @@ -1,5 +1,6 @@ +#!/usr/bin/env cwl-runner +cwlVersion: v1.2 class: CommandLineTool -cwlVersion: v1.0 baseCommand: ["sh", "example.sh"] requirements: diff --git a/src/_includes/cwl/custom-types/custom-types.cwl b/src/_includes/cwl/custom-types/custom-types.cwl old mode 100644 new mode 100755 index 707d5c2a..d60e6e92 --- a/src/_includes/cwl/custom-types/custom-types.cwl +++ b/src/_includes/cwl/custom-types/custom-types.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool requirements: diff --git a/src/_includes/cwl/conformance-test.yml b/src/_includes/cwl/cwl_tests.yml similarity index 100% rename from src/_includes/cwl/conformance-test.yml rename to src/_includes/cwl/cwl_tests.yml diff --git a/src/_includes/cwl/environment-variables/env.cwl b/src/_includes/cwl/environment-variables/env.cwl index 7e4d4087..6162a04c 100755 --- a/src/_includes/cwl/environment-variables/env.cwl +++ b/src/_includes/cwl/environment-variables/env.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: env requirements: diff --git a/src/_includes/cwl/expressions/expression.cwl b/src/_includes/cwl/expressions/expression.cwl old mode 100644 new mode 100755 index da1e75dc..a04695bb --- a/src/_includes/cwl/expressions/expression.cwl +++ b/src/_includes/cwl/expressions/expression.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: echo diff --git a/src/_includes/cwl/file-formats/metadata_example.cwl b/src/_includes/cwl/file-formats/metadata_example.cwl old mode 100644 new mode 100755 index 9485522b..bcaaff70 --- a/src/_includes/cwl/file-formats/metadata_example.cwl +++ b/src/_includes/cwl/file-formats/metadata_example.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: An example tool demonstrating metadata. diff --git a/src/_includes/cwl/inputs/array-inputs.cwl b/src/_includes/cwl/inputs/array-inputs.cwl index bef63538..0e5d6e44 100755 --- a/src/_includes/cwl/inputs/array-inputs.cwl +++ b/src/_includes/cwl/inputs/array-inputs.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool inputs: filesA: diff --git a/src/_includes/cwl/inputs/inp.cwl b/src/_includes/cwl/inputs/inp.cwl index 576c16da..20ac1d79 100755 --- a/src/_includes/cwl/inputs/inp.cwl +++ b/src/_includes/cwl/inputs/inp.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: echo inputs: diff --git a/src/_includes/cwl/inputs/record.cwl b/src/_includes/cwl/inputs/record.cwl index e33cb44a..e69a1ac9 100755 --- a/src/_includes/cwl/inputs/record.cwl +++ b/src/_includes/cwl/inputs/record.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool inputs: dependent_parameters: diff --git a/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl b/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl old mode 100644 new mode 100755 index 745c1779..ca2b59bd --- a/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl +++ b/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: An example tool demonstrating metadata. diff --git a/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl b/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl old mode 100644 new mode 100755 index 09d31e4a..e30a3c64 --- a/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl +++ b/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: An example tool demonstrating metadata. diff --git a/src/_includes/cwl/outputs/array-outputs.cwl b/src/_includes/cwl/outputs/array-outputs.cwl index 2d6654ea..9d7d8022 100755 --- a/src/_includes/cwl/outputs/array-outputs.cwl +++ b/src/_includes/cwl/outputs/array-outputs.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: touch inputs: diff --git a/src/_includes/cwl/outputs/stdout.cwl b/src/_includes/cwl/outputs/stdout.cwl index 5908f88f..53e2db0e 100755 --- a/src/_includes/cwl/outputs/stdout.cwl +++ b/src/_includes/cwl/outputs/stdout.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: echo stdout: output.txt diff --git a/src/_includes/cwl/outputs/tar.cwl b/src/_includes/cwl/outputs/tar.cwl old mode 100644 new mode 100755 index f1b45964..187fe05f --- a/src/_includes/cwl/outputs/tar.cwl +++ b/src/_includes/cwl/outputs/tar.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: [tar, --extract] inputs: diff --git a/src/_includes/cwl/parameter-references/tar-param.cwl b/src/_includes/cwl/parameter-references/tar-param.cwl index 87ad9e0f..913b7fdd 100644 --- a/src/_includes/cwl/parameter-references/tar-param.cwl +++ b/src/_includes/cwl/parameter-references/tar-param.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: [tar, --extract] inputs: diff --git a/src/_includes/cwl/specifying-software-requirements/custom-types.cwl b/src/_includes/cwl/specifying-software-requirements/custom-types.cwl old mode 100644 new mode 100755 index 044db0bf..70cb9dee --- a/src/_includes/cwl/specifying-software-requirements/custom-types.cwl +++ b/src/_includes/cwl/specifying-software-requirements/custom-types.cwl @@ -1,4 +1,5 @@ -cwlVersion: v1.0 +#!/usr/bin/env cwl-runner +cwlVersion: v1.2 class: CommandLineTool label: "InterProScan: protein sequence classifier" diff --git a/src/_includes/cwl/staging-input-files/linkfile.cwl b/src/_includes/cwl/staging-input-files/linkfile.cwl old mode 100644 new mode 100755 index ffeb6996..43cf79bc --- a/src/_includes/cwl/staging-input-files/linkfile.cwl +++ b/src/_includes/cwl/staging-input-files/linkfile.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool hints: DockerRequirement: diff --git a/src/_includes/cwl/using-containers/docker.cwl b/src/_includes/cwl/using-containers/docker.cwl index 9f6090a1..35c5e842 100755 --- a/src/_includes/cwl/using-containers/docker.cwl +++ b/src/_includes/cwl/using-containers/docker.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: node hints: diff --git a/src/_includes/cwl/workflows/1st-workflow.cwl b/src/_includes/cwl/workflows/1st-workflow.cwl old mode 100644 new mode 100755 index 24b19bd2..4da55143 --- a/src/_includes/cwl/workflows/1st-workflow.cwl +++ b/src/_includes/cwl/workflows/1st-workflow.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow inputs: tarball: File diff --git a/src/_includes/cwl/workflows/arguments.cwl b/src/_includes/cwl/workflows/arguments.cwl old mode 100644 new mode 100755 index c26d2642..ff80076a --- a/src/_includes/cwl/workflows/arguments.cwl +++ b/src/_includes/cwl/workflows/arguments.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: Example trivial wrapper for Java 9 compiler hints: diff --git a/src/_includes/cwl/workflows/hello_world.cwl b/src/_includes/cwl/workflows/hello_world.cwl index 48e2f792..1c39bca4 100755 --- a/src/_includes/cwl/workflows/hello_world.cwl +++ b/src/_includes/cwl/workflows/hello_world.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: echo inputs: diff --git a/src/_includes/cwl/workflows/hello_world_to_stdout.cwl b/src/_includes/cwl/workflows/hello_world_to_stdout.cwl index 1d550fc2..39e8e2d4 100755 --- a/src/_includes/cwl/workflows/hello_world_to_stdout.cwl +++ b/src/_includes/cwl/workflows/hello_world_to_stdout.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: echo inputs: diff --git a/src/_includes/cwl/workflows/nestedworkflows.cwl b/src/_includes/cwl/workflows/nestedworkflows.cwl old mode 100644 new mode 100755 index 75a4f00a..c43e5096 --- a/src/_includes/cwl/workflows/nestedworkflows.cwl +++ b/src/_includes/cwl/workflows/nestedworkflows.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow inputs: [] diff --git a/src/_includes/cwl/workflows/scatter-nested-workflow.cwl b/src/_includes/cwl/workflows/scatter-nested-workflow.cwl old mode 100644 new mode 100755 index 9b2f6aa6..7bc6c1d7 --- a/src/_includes/cwl/workflows/scatter-nested-workflow.cwl +++ b/src/_includes/cwl/workflows/scatter-nested-workflow.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: diff --git a/src/_includes/cwl/workflows/scatter-two-steps.cwl b/src/_includes/cwl/workflows/scatter-two-steps.cwl old mode 100644 new mode 100755 index 57b9ca2e..c2963cfc --- a/src/_includes/cwl/workflows/scatter-two-steps.cwl +++ b/src/_includes/cwl/workflows/scatter-two-steps.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: diff --git a/src/_includes/cwl/workflows/scatter-workflow.cwl b/src/_includes/cwl/workflows/scatter-workflow.cwl old mode 100644 new mode 100755 index 80a334f3..954e1660 --- a/src/_includes/cwl/workflows/scatter-workflow.cwl +++ b/src/_includes/cwl/workflows/scatter-workflow.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: diff --git a/src/_includes/cwl/workflows/tar-param.cwl b/src/_includes/cwl/workflows/tar-param.cwl old mode 100644 new mode 100755 index 87ad9e0f..913b7fdd --- a/src/_includes/cwl/workflows/tar-param.cwl +++ b/src/_includes/cwl/workflows/tar-param.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: [tar, --extract] inputs: diff --git a/src/_includes/cwl/workflows/wc-tool.cwl b/src/_includes/cwl/workflows/wc-tool.cwl index c3064634..397df77e 100755 --- a/src/_includes/cwl/workflows/wc-tool.cwl +++ b/src/_includes/cwl/workflows/wc-tool.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: wc arguments: ["-c"] diff --git a/src/_static/css/custom.css b/src/_static/css/custom.css new file mode 100644 index 00000000..9f53adff --- /dev/null +++ b/src/_static/css/custom.css @@ -0,0 +1,10 @@ +body { + /* + * These settings are copied from the https://commonwl.org website style + * for consistency. + */ + font-family: system-ui, -apple-system, "Segoe UI", Roboto, "Helvetica Neue", Arial, "Noto Sans", "Liberation Sans", sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol", "Noto Color Emoji"; + font-size: 16px; + line-height: 24px; + color: rgb(33, 37, 41); +} diff --git a/src/_templates/sidebar-nav-bs.html b/src/_templates/sidebar-nav-bs.html index 73c66bee..a559969d 100644 --- a/src/_templates/sidebar-nav-bs.html +++ b/src/_templates/sidebar-nav-bs.html @@ -1,11 +1,8 @@ diff --git a/src/conf.py b/src/conf.py index c893d8a5..bcfe20a8 100644 --- a/src/conf.py +++ b/src/conf.py @@ -157,6 +157,10 @@ # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] +html_css_files = [ + 'css/custom.css', +] + html_logo = '_static/images/logos/cwl/CWL-Logo-HD-cropped2.png' html_favicon = '_static/images/favicons/cwl/favicon.ico' @@ -167,6 +171,10 @@ ] html_theme_options = { + "external_links": [ + {"name": "Community", "url": "https://www.commonwl.org/community/"}, + ], + "header_links_before_dropdown": 6, "icon_links": [ { "name": "GitHub", @@ -226,3 +234,89 @@ "doc_path": "src", "default_mode": "light" } + +gettext_uuid = True +gettext_compact = "user_guide" +locale_dirs = ['../locales/'] + + +# Patched MyST parser +# from __future__ import annotations + +from docutils import nodes +from docutils.parsers.rst import Parser as RstParser +from sphinx.parsers import Parser as SphinxParser +from sphinx.util import logging + +from myst_parser.config.main import ( + MdParserConfig, + TopmatterReadError, + merge_file_level, + read_topmatter, +) +from myst_parser.mdit_to_docutils.sphinx_ import SphinxRenderer, create_warning +from myst_parser.parsers.mdit import create_md_parser + +SPHINX_LOGGER = logging.getLogger(__name__) + +class MystParser(SphinxParser): + """Sphinx parser for Markedly Structured Text (MyST).""" + + supported: tuple[str, ...] = ("md", "markdown", "myst") + """Aliases this parser supports.""" + + settings_spec = RstParser.settings_spec + """Runtime settings specification. + Defines runtime settings and associated command-line options, as used by + `docutils.frontend.OptionParser`. This is a concatenation of tuples of: + - Option group title (string or `None` which implies no group, just a list + of single options). + - Description (string or `None`). + - A sequence of option tuples + """ + + config_section = "myst parser" + config_section_dependencies = ("parsers",) + translate_section_name = None + + def parse(self, inputstring: str, document: nodes.document) -> None: + """Parse source text. + :param inputstring: The source string to parse + :param document: The root docutils node to add AST elements to + """ + # get the global config + config: MdParserConfig = document.settings.env.myst_config + + # update the global config with the file-level config + try: + topmatter = read_topmatter(inputstring) + except TopmatterReadError: + pass # this will be reported during the render + else: + if topmatter: + warning = lambda wtype, msg: create_warning( # noqa: E731 + document, msg, line=1, append_to=document, subtype=wtype + ) + config = merge_file_level(config, topmatter, warning) + + parser = create_md_parser(config, SphinxRenderer) + # TODO: In the first pass, the call above will use MarkdownIt over the whole document, + # populating the ``.md_env`` correctly. Over the next passes, from transforms as + # ``sphinx.transforms.i18n.Locale`` it will create a blank new document, as well + # as a new MarkdownIT parser but using just the Docutils document that is being + # translated. As a result of this, the translation has no reference-links, and it + # gives you the translation without resolving the links. Here we just re-use the + # ``md_env`` dictionary that contains the ``.references`` populated in the first + # pass, fixing i18n with MyST Parser. + env = {} if not hasattr(document.settings, 'md_env') else document.settings.md_env + parser.options["document"] = document + parser.render(inputstring, env) + document.settings.md_env = parser.renderer.md_env + + +def setup(app): + """Sphinx setup callback.""" + + # TODO: Here we replace the MySTParser (that replaces the Sphinx default parser...), + # with our patched version above. + app.add_source_parser(MystParser, override=True) diff --git a/src/faq.md b/src/faq.md index 8e7f41a2..50843d6a 100644 --- a/src/faq.md +++ b/src/faq.md @@ -8,7 +8,7 @@ :backlinks: "top" ``` -## Non "`File`" types using `evalFrom` +## Non "`File`" Types Using `evalFrom` ```yaml cwlVersion: v1.0 # or v1.1 @@ -38,12 +38,12 @@ outputs: outputEval: $(self[0].contents) ``` -## Rename an input file +## Rename an Input File -This example shows how you can change the name of an input file +This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another -step in a workflow and don't want to work with the default names that these +step in a workflow, and don't want to work with the default names that these files were given when they were created. ```yaml @@ -56,9 +56,9 @@ requirements: entryName: $(inputs.src1.basename)_custom_extension ``` -## Rename an output file +## Rename an Output File -This example shows how you can change the name of an output file +This example demonstrates how to change the name of an output file from the default name given to it by a tool: ```yaml @@ -79,7 +79,63 @@ outputs: outputEval: ${self[0].basename=inputs.otu_table_name; return self;} ``` -## Setting `self`-based input bindings for optional inputs +## Referencing a Local Script + +There are two ways to reference a local script: + +The first method involves adding the folder containing your scripts to the `PATH` environment variable. +This allows you to run the shell script directly without using `sh` or `bash` commands. + +Start with adding a _shebang_ at the top of your file: + +```{code-block} +#!/bin/bash +``` + +After that, make the script executable with the command `chmod +x scriptname.sh` + +Finally, modify your `PATH` to add the directory where your script is located. +(It is good practice to use `$HOME/bin` for storing your own scripts). + +```bash +export PATH=$PATH:$HOME/bin +``` + +Now you can use `baseCommand: scriptname.sh` to run the script directly. + +```cwl +#!/bin/bash +cwlVersion: v1.0 +class: CommandLineTool +baseCommand: scriptname.sh +``` + +When you wish to share your work later, you can place your script in a software container in the Docker format. + +The second method involves including an input of `type: File` in the script itself: + +```cwl +class: CommandLineTool + +inputs: + my_script: + type: File + inputBinding: + position: 0 + + + # other inputs go here + +baseCommand: sh + +outputs: [] +``` + +```{note} +In CWL, everything must be directly stated. +``` + +## Setting `self`-based Input Bindings for Optional Inputs Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. @@ -106,10 +162,10 @@ baseCommand: echo outputs: [] ``` -## Model a "one-or-the-other" parameter +## Model a "one-or-the-other" Parameter -Below is an example of how -you can specify different strings to be added to a command line +Below is an example showing how +to specify different strings to be added to a command line, based on the value given to a Boolean parameter. ```yaml @@ -129,7 +185,7 @@ baseCommand: echo outputs: [] ``` -## Connect a solo value to an input that expects an array of that type +## Connect a Solo Value to an Input that Expects an Array of that Type Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with @@ -191,7 +247,7 @@ inputs: ## Enum Inputs ⚜️ -For command-line flags that require a specific input as the argument, an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.** +For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.** ```yaml Format: @@ -211,7 +267,7 @@ Format: ## Record Inputs 📀 -For command-line flags that are either **mutually exclusive** or **dependent**, a special record type can be defined. You can also specify null here to create optional inputs. +For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs. ```yaml #Using record inputs to create mutually exclusive inputs @@ -265,7 +321,7 @@ For command-line flags that are either **mutually exclusive** or **dependent**, ``` ## Setting Mutually Exclusive Parameters -In order to properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline javascript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value. +To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value. ```yaml steps: @@ -300,7 +356,7 @@ input: My String: $(input.stringvalue) ``` -## `cwltool` errors due to filenames with space characters inside +## `cwltool` Errors due to Filenames with Space Characters Inside `cwltool` does not allow some characters in filenames by default. @@ -314,7 +370,7 @@ Invalid filename: 'a space is here.txt' contains illegal characters If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`. -## CWL Parameter Reference error due to hyphen in input identifier +## CWL Parameter Reference Error due to Hyphen in Input Identifier If `cwltool --validate` returns valid @@ -391,7 +447,7 @@ The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards. -## Debug JavaScript expressions +## Debug JavaScript Expressions You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it diff --git a/src/introduction/basic-concepts.md b/src/introduction/basic-concepts.md index 30459c8a..33f1ced7 100644 --- a/src/introduction/basic-concepts.md +++ b/src/introduction/basic-concepts.md @@ -1,13 +1,13 @@ # Basic Concepts -This section describes the basic concepts for users to get started working with +This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar -with workflow managers, YAML, and comfortable following instructions for the -command-line. The other sections of the user guide cover the same concepts but -in more detail. If you are already familiar with CWL or looking for more advanced +with workflow managers, YAML, and comfortable with following instructions for the +command-line. The other sections of the user guide cover the same concepts, but +in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section. -## The CWL specification +## The CWL Specification ```{include} /_includes/what-is-cwl.md ``` @@ -22,9 +22,9 @@ The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}. -The specification version can have up to three numbers separated by `.`'s (dots). +The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like -the removal of deprecated features. The second is the minor release number, +the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification. @@ -37,7 +37,7 @@ the end of this section to [learn more](#learn-more) about it. ## Implementations An implementation of the CWL specification is any software written following -what is defined in a version of the specification document. Implementations may +what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses. @@ -47,6 +47,7 @@ in parallel across many nodes. % TODO: add a link to the Core Concepts -> Requirements section below? + ```{graphviz} :name: specification-and-implementations-graph :caption: CWL specification, implementations, and other tools. @@ -108,10 +109,10 @@ behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}: -- A command-line tool; -- An expression tool; -- An operation; -- And a workflow. +- A command-line tool. +- An expression tool. +- An operation. +- A workflow. {{ CWL_PROCESSING_UNITS_GRAPH }} @@ -120,26 +121,26 @@ A command-line tool is a wrapper for a command-line utility like `echo`, An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common -parts of a workflow execution into reusable JavaScript code, that +parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool. +Operation is an abstract process that also takes inputs, produces +outputs, and can be used in a workflow. But it is a special operation +not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide. + The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. -The inputs of a workflow can be passed to any of its steps, and +The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow. -Operation is an abstract process that also takes inputs, produces -outputs, and can be used in a workflow. But it is a special operation -not so commonly used. It is discussed in another section. - The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance: -- `InlineJavascriptWorkflow`, enables JavaScript in expressions. -- `SubworkflowFeatureRequirement`, enables nested workflows. -- `InitialWorkDirRequirement`, controls staging files in the input directory. +- `InlineJavascriptWorkflow` - enables JavaScript in expressions. +- `SubworkflowFeatureRequirement` - enables nested workflows. +- `InitialWorkDirRequirement` - controls staging files in the input directory. Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the @@ -149,32 +150,32 @@ runners. Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained -in detail in another section. +in detail in the [Requirements](../topics/requirements-and-hints.md) section. -## FAIR workflows +## FAIR Workflows > The FAIR principles have laid a foundation for sharing and publishing -> digital assets and, in particular, data. The FAIR principles emphasize +> digital assets, and in particular, data. The FAIR principles emphasize > machine accessibility and that all digital assets should be Findable, > Accessible, Interoperable, and Reusable. Workflows encode the methods > by which the scientific process is conducted and via which data are -> created. It is thus important that workflows both support the creation -> of FAIR data and themselves adhere to the FAIR principles. +> created. It is thus important that workflows support the creation +> of FAIR data and adhere to the FAIR principles. > — [FAIR Computational Workflows](https://workflows.community/groups/fair/), > Workflows Community Initiative. CWL has roots in "make" and many similar tools that determine order of -execution based on dependencies between tasks. However, unlike "make", CWL +execution, based on dependencies between tasks. However, unlike "make", CWL tasks are isolated, and you must be explicit about your inputs and outputs. The benefit of explicitness and isolation are flexibility, portability, and -scalability: tools and workflows described with CWL can transparently leverage +scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors. `cwltool` also uses the PROV-O standard ontology for data provenance. -## Learn more +## Learn More - Semantic Versioning - - The CWL Specification page in the CWL website: diff --git a/src/introduction/prerequisites.md b/src/introduction/prerequisites.md index f739add6..afd26dd1 100644 --- a/src/introduction/prerequisites.md +++ b/src/introduction/prerequisites.md @@ -1,18 +1,18 @@ # Prerequisites -% This page supersedes the old setup.md. We used that page as reference while +% This page supersedes the old setup page: setup.md. We used that page as a reference while % writing this documentation. The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, -`cwltool`. You can use another CWL compatible runner or workflow systems but the results and +`cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical). ```{admonition} CWL Implementations -There are many implementations of the CWL standards. Some are complete CWL runners, -others are plug-ins or extensions to workflow engines. We have a better +There are many implementations of the CWL standards. Some are complete CWL runners, while +others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section. ``` @@ -26,13 +26,13 @@ of the following options for your operating system: - Windows ```{note} -If you are using Windows, you will have to install the Windows Subsystem for Linux 2. +If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+). ``` -## CWL runner +## CWL Runner % https://github.com/common-workflow-language/user_guide/issues/166 % https://github.com/common-workflow-language/user_guide/issues/64 @@ -52,18 +52,17 @@ environment: :name: installing-cwltool-with-pip-and-venv :caption: Installing `cwltool` with `pip` and `venv`. -$ python -m venv venv +$ python3 -m venv venv $ source venv/bin/activate $ (venv) pip install -U pip setuptools wheel $ (venv) pip install cwltool ``` ```{note} -You can find the `cwl-runner` source code [here](https://github.com/common-workflow-language/cwltool/tree/main/cwlref-runner). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`. ``` -Let's use a simple CWl tool description `true.cwl` with `cwltool`. +Let's use a simple CWL tool description `true.cwl` with `cwltool`. ```{literalinclude} /_includes/cwl/true.cwl :language: yaml @@ -71,10 +70,10 @@ Let's use a simple CWl tool description `true.cwl` with `cwltool`. :name: true.cwl ``` -The `cwltool` command has an option to validate CWL tool and workflow descriptionss. It will parse the -CWL document, look for syntax errors, and verify that the descriptions are compliant -with the CWL standards, without running it. To validate CWL workflows (or even a -standalone command line tool description like above) pass the `--validate` option +The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the +CWL document, look for syntax errors, and verify that the workflow descriptions are compliant +with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a +standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command: ```{runcmd} cwltool --validate true.cwl @@ -89,11 +88,14 @@ You can run the CWL tool description by omitting the `--validate` option: :caption: Running `true.cwl` with `cwltool`. ``` -### cwl-runner Python module +### Cwl-runner Python Module -`cwl-runner` is an implementation-agnostic alias for CWL Runners. +`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means +that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular +CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` -directly. The `cwl-runner` alias command then chooses the correct CWL runner. +directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred +CWL implementation. This is convenient for environments with multiple CWL runners. The CWL community publishes a Python package with the name `cwlref-runner` that installs @@ -106,7 +108,7 @@ an alias for `cwltool` under the name `cwl-runner` $ pip install cwlref-runner ``` -Now you can validate and run your workflow with `cwl-runner` executable, +Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section. @@ -120,9 +122,9 @@ as in the previous section. :caption: Running `true.cwl` with `cwl-runner`. ``` -Another way to execute `cwl-runner` is invoking the file directly. For that, -the first thing you need to copy `true.cwl` workflow into a new file -`true_shebang.cwl` and include a special first line, a *shebang*: +Another way to execute `cwl-runner` is by invoking the file directly. For that, +the first thing you need to do is copy `true.cwl` workflow into a new file: +`true_shebang.cwl`, and include a special first line, a *shebang*: ```{literalinclude} /_includes/cwl/true_shebang.cwl :language: cwl @@ -139,7 +141,7 @@ Now you can make the file `true_shebang.cwl` executable with `chmod u+x`. $ chmod u+x true.cwl ``` -And finally you can execute it directly in the command-line and the program +And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file. @@ -152,9 +154,8 @@ rest of the file. The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is -considered a good practice to use `/usr/bin/env ` since it -looks for the `` program in the system `PATH`, instead of -using a hard-coded location. +considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` +looks for the `` program in the system `PATH`, ``` ## Text Editor @@ -164,7 +165,7 @@ an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs. There are extensions for Visual Studio Code and WebStorm that provide -integration with CWL, with customized syntax highlighting and better +integration with CWL, and features such as customized syntax highlighting and better auto-complete: - Visual Studio Code with the Benten (CWL) plugin - @@ -182,7 +183,7 @@ Follow the instructions in the Docker documentation to install it for your operating system: . You do not need to know how to write and build Docker containers. In the -rest of the user guide we will use existing Docker images for running +rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers. @@ -192,7 +193,7 @@ Singularity. You can also use alternative container registries for pulling images. ``` -## Learn more +## Learn More - The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts. - The Python `venv` module: diff --git a/src/introduction/quick-start.md b/src/introduction/quick-start.md index 98476fcf..84d52dc9 100644 --- a/src/introduction/quick-start.md +++ b/src/introduction/quick-start.md @@ -11,7 +11,7 @@ must be comfortable following instructions for the command-line. CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated -with comments: +with comments. Note that comments start with `#`: ```{literalinclude} /_includes/cwl/hello_world.cwl :language: cwl @@ -29,7 +29,7 @@ for the sake of simplicity, we are using the term “workflow” here. You will more about this in the [basic concepts](basic-concepts.md) section. ``` -## Installing a CWL runner +## Installing a CWL Runner `cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the @@ -91,7 +91,7 @@ a requirement. You can choose any name for your workflows and Inputs Object files. ``` -## Learn more +## Learn More Continue reading the next sections of this User Guide! - [List of CWL Implementations](https://www.commonwl.org/implementations). diff --git a/src/topics/best-practices.md b/src/topics/best-practices.md index fe0d663f..4c2e18ab 100644 --- a/src/topics/best-practices.md +++ b/src/topics/best-practices.md @@ -1,8 +1,8 @@ # Best Practices -Below are a set of recommended good practices to keep in mind when writing a +The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines -are presented for consideration on a scale of usefulness: more is better, not +are presented for consideration on a scale of usefulness: although more is better, not all are required. - No `type: string` parameters for names of input or reference @@ -10,15 +10,15 @@ all are required. - A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this - document. For example if the workflow is shared publicly, licensing terms have to be clear so that - a future user can understand under what conditions they can run the workflow, modify it and/or - combine it with other workflows. For this reason please consider including a license field in the + document. For example, if the workflow is shared publicly, licensing terms must be clear so that + a future user understands under what conditions they can run the workflow, modify it and/or + combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]. If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. - Construct the metadata field for the licence by providing a URL of the form + Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license. @@ -38,7 +38,7 @@ all are required. [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md). - Include [attribution information][license-example] for the author(s) of - the CWL tool or workflow description. Use unambiguous identifiers like + the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]. - In tool descriptions, list dependencies using short name(s) under @@ -60,7 +60,7 @@ all are required. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: "https://www.iana.org/assignments/media-types/" }`. [Full IANA media type list][iana-types] (also known as MIME types). For - non-bioinformatics tools use or build an appropriate ontology/controlled + non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it. - Mark all input and output `File`s that are read from or written to in a @@ -68,15 +68,15 @@ all are required. - Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your - tool descriptions with options that you don't need/use. + tool descriptions with options that you don't need or use. - Custom types should be defined with one external YAML per type definition for re-use. -- Include a top level short `label` summarising the tool/workflow. +- Include a top-level short `label` summarising the tool/workflow. -- If useful, include a top level `doc` as well. This should provide a - longer, more detailed description than was provided in the top level `label` +- If useful, include a top-level `doc` as well. This should provide a + longer, more detailed description than was provided in the top-level `label` (see above). - Use `type: enum` instead of `type: string` for elements with a fixed diff --git a/src/topics/command-line-tool.md b/src/topics/command-line-tool.md index 2977e3a1..1aea6311 100644 --- a/src/topics/command-line-tool.md +++ b/src/topics/command-line-tool.md @@ -63,3 +63,23 @@ and in the [Outputs](../topics/outputs.md) sections. % % - Spaces in commands https://github.com/common-workflow-language/user_guide/issues/39 % - Arguments (tell the reader the different use cases for arguments and inputs, tell them there is a section about inputs) + + +## Network Access +This indicates whether a process requires outgoing IPv4/IPv6 network access. +If a command-line tool is written manually in CWL v1.1+, there is a need to +specify when network access is required. + +```cwl +cwlVersion: v1.2 +class: CommandLineTool + +requirements: + NetworkAccess: + networkAccess: true +``` + +```{note} +CWL v1.0 command-line tools that are upgraded to v1.1 +or v1.2 get Network Access automatically. +``` diff --git a/src/topics/custom-types.md b/src/topics/custom-types.md index f0b59caf..e4c47a59 100644 --- a/src/topics/custom-types.md +++ b/src/topics/custom-types.md @@ -7,7 +7,7 @@ customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly. The example below is a CWL description of the [biom convert format][biom] tool for -converting a standard biom table file to hd5 format. +converting a standard biom table file to hdf5 format. ```{literalinclude} /_includes/cwl/custom-types/custom-types.cwl :language: cwl @@ -21,7 +21,7 @@ converting a standard biom table file to hd5 format. :name: custom-types.yml ``` -___Note:___ To follow the example below, you need to [download the example input file](https://raw.githubusercontent.com/common-workflow-language/user_guide/main/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`: +___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`: ```{code-block} console $ wget https://github.com/common-workflow-language/user_guide/raw/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom @@ -48,7 +48,7 @@ the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that -tells the tool to create an OTU table in hd5 format. +tells the tool to create an OTU table in hdf5 format. The contents of the YAML file describing the custom type are given below: diff --git a/src/topics/expressions.md b/src/topics/expressions.md index eebc027b..4c034a7f 100644 --- a/src/topics/expressions.md +++ b/src/topics/expressions.md @@ -113,7 +113,7 @@ only in certain fields. These are: [file-prop]: https://www.commonwl.org/v1.0/CommandLineTool.html#File -## Using external libraries and inline JavaScript code with `expressionLib` +## Using External Libraries and Inline JavaScript Code with `expressionLib` The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript diff --git a/src/topics/operations.md b/src/topics/operations.md index 19f8c817..b6afca2a 100644 --- a/src/topics/operations.md +++ b/src/topics/operations.md @@ -1,6 +1,6 @@ # Operations -Operation is a type of CWL process just like a workflow, a command line tool, or +An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed. @@ -14,7 +14,7 @@ you are ready to submit the workflow to a CWL runner: ``` The `uppercase` step of the workflow is an operation. It can be used like -use a command line tool or an expression. You can also plot it with the +a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`: ```{runcmd} cwltool --print-dot operations.cwl @@ -52,7 +52,7 @@ style=dashed; } ``` -If you try running it with `cwltool` the command will fail, since `cwltool` +If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it: ```{runcmd} cwltool operations.cwl --message Hello diff --git a/src/topics/using-containers.md b/src/topics/using-containers.md index 903e6fdc..90a3f0bb 100644 --- a/src/topics/using-containers.md +++ b/src/topics/using-containers.md @@ -41,7 +41,7 @@ hints: dockerPull: node:slim ``` -`baseCommand: node` tells CWL that we will be running this command in a container. We +`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, @@ -49,7 +49,7 @@ the name of the container image (you can even specify the tag, which is good ide best practices when using containers for reproducible research). In this case we have used a container called `node:slim`. -Provide a "hello.js" and invoke `cwltool` providing the tool description and the +Create a Javascript file named "hello.js" and invoke `cwltool` providing the tool description and the input object on the command line: ```{literalinclude} /_includes/cwl/using-containers/hello.js diff --git a/src/topics/yaml-guide.md b/src/topics/yaml-guide.md index 6d05c6ed..9475f83a 100644 --- a/src/topics/yaml-guide.md +++ b/src/topics/yaml-guide.md @@ -5,7 +5,7 @@ [YAML][yaml] is a file format designed to be readable by both computers and humans. -This guide introduces the features of YAML +This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files. ```{note} @@ -25,9 +25,9 @@ You can skip this section if you are already comfortable with YAML. Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, -where whitespace after the `:` is optional. +where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - -We use [_camelCase_][camelCase] for multi-word key names +[_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example: @@ -48,7 +48,7 @@ numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below). -Values may be wrapped in quotation marks +Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `"1234"` will be treated as a character string , while `1234` will be treated as an integer. @@ -80,7 +80,7 @@ be sure to add at least one space before the `#`! When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. -Called _maps_, +Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as "children") are written @@ -101,7 +101,7 @@ inputs: # this key has an object value prefix: -f ``` -The YAML above illustrates how you can build up complex nested object +The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, @@ -126,7 +126,7 @@ graph TD ## Arrays -In certain circumstances it is necessary to provide +In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. @@ -166,8 +166,8 @@ exclusive_parameters: ## JSON Style -YAML is based on [JavaScript Object Notation (JSON)][json] -and maps and arrays can also be defined in YAML using the native JSON syntax. +YAML is based on [JavaScript Object Notation (JSON)][json]. +Maps and arrays can also be defined in YAML using the native JSON syntax. For example: ```yaml @@ -182,13 +182,13 @@ inputs: {example_flag: {type: boolean, inputBinding: {position: 1, prefix: -f}}} ``` Native JSON can be useful -to indicate where a field is being left intentionally empty +in indicating where a field is intentionally left empty (such as `[]` for an empty array), -and where it makes more sense +as well as where it makes more sense for the values to be located on the same line -(such as when providing option flags and their values in a shell command). +(For example, when providing option flags and their values in a shell command). However, as the second example above shows, -it can severely affect the readability of a YAML file +it can severely affect the readability of a YAML file, and should be used sparingly. ## Reference