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README.md

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@@ -123,16 +123,15 @@ $ miniwdl cromwell hello.wdl who=Alyssa "who=Ben Bitdiddle" x=41
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}
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```
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By first analyzing the WDL code, this tool translates the freeform command-line arguments into appropriately-typed JSON inputs for Cromwell. It downloads the Cromwell JAR file automatically to a temporary location; a compatible `java` JRE must be available to run it, and the invoking [user must have permission to control Docker](https://docs.docker.com/install/linux/linux-postinstall/). You can use the `-r/--jar` option if you already have a local copy of Cromwell; other Cromwell configuration options are available (see `--help`).
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The outputs and logs are written to a new date/time-named subdirectory of the current working directory (overridable; see `--help`).
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By first analyzing the WDL code, this tool translates the freeform command-line arguments into appropriately-typed JSON inputs for Cromwell. It downloads the Cromwell JAR file automatically to a temporary location; a compatible `java` JRE must be available to run it. You can use the `-r/--jar` option if you already have a local copy of Cromwell; other Cromwell configuration options are available (see `--help`). The invoking user must have [permission to control Docker](https://docs.docker.com/install/linux/linux-postinstall/#manage-docker-as-a-non-root-user).
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The tool supports shell tab-completion for the workflow's available input names. To use this, enable [argcomplete](https://argcomplete.readthedocs.io/en/latest/) global completion by invoking `activate-global-python-argcomplete` and starting a new shell session. Then, start a command line `miniwdl cromwell hello.wdl ` and try double-tab.
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### `miniwdl run`
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miniwdl's built-in capability to execute workflows on the local host is in early testing. The [Releases](https://github.com/chanzuckerberg/miniwdl/releases) page documents current salient limitations. If you encounter an interoperability problem not mentioned there, we want to hear about it via [Issues](https://github.com/chanzuckerberg/miniwdl/issues)!
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Operation is nearly identical to `miniwdl cromwell`. The invoking [user must have permission to control Docker](https://docs.docker.com/install/linux/linux-postinstall/).
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Operation is nearly identical to `miniwdl cromwell`. The invoking user must have [permission to control Docker](https://docs.docker.com/install/linux/linux-postinstall/#manage-docker-as-a-non-root-user).
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```
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$ miniwdl run hello.wdl who=Alyssa "who=Ben Bitdiddle" x=41
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1. `git clone --recursive` this repository
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2. Install dependencies as illustrated in the [Dockerfile](https://github.com/chanzuckerberg/miniwdl/blob/master/Dockerfile) (OS packages + PyPI packages listed in `requirements.txt` and `requirements.dev.txt`)
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3. Invoking user must be able to [access local Docker daemon](https://docs.docker.com/install/linux/linux-postinstall/#manage-docker-as-a-non-root-user).
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3. Invoking user must have [permission to control Docker](https://docs.docker.com/install/linux/linux-postinstall/#manage-docker-as-a-non-root-user).
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The Makefile has a few typical scripted flows:
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- `make pretty` reformats the code with [black](https://github.com/python/black)
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- `make check` validates the code with [Pylint](https://www.pylint.org/) and [Pyre](https://pyre-check.org/)
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As the test suite takes several minutes to run, you can e.g. `python3 -m unittest -f tests/test_5stdlib.py` to run relevant subsets.
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To quickly run only a relevant subset of the tests, you can e.g. `python3 -m unittest -f tests/test_5stdlib.py`. To invoke the command-line interface (`miniwdl` command once installed), e.g. `python3 -m WDL check ...` or `python3 -m WDL run ...`.
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## Security
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WDL/CLI.py

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def fill_run_subparser(subparsers):
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run_parser = subparsers.add_parser("run", help="Run task locally [alpha test]")
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run_parser = subparsers.add_parser(
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"run", help="Run workflow/task locally with built-in runtime [alpha test]"
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)
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run_parser.add_argument("uri", metavar="URI", type=str, help="WDL document filename/URI")
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run_parser.add_argument(
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"inputs",

requirements.txt

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lark-parser==0.7.1
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docker
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argcomplete
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pygtail==0.11.0
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pygtail>=0.11.0

setup.cfg

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[metadata]
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name = miniwdl
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description = Workflow Description Language (WDL) static analysis toolkit
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description = Workflow Description Language (WDL) developer toolkit
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description-file = README.md
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description-content-type = text/markdown; charset=UTF-8
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author = CZI

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