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‎.gitignore

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README.html
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README_files/
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*.DS_Store
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*__pycache__
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*.h5ad
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changelogs
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# IDE ignores
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/.idea/
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/.vscode/
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# repo specific ignores
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output_bash
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# R specific ignores
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.Rhistory
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.Rproj.user
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*.Rproj
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# viash specific ignores
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docker_output/
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check_results/
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log.txt
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.viash*
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/resources/
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/resources_test/
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# nextflow specific ignores
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/.nextflow*
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/work
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output

‎.nojekyll

Whitespace-only changes.

‎CHANGELOG.md

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‎CODE_OF_CONDUCT.md

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# Contributor Covenant Code of Conduct
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## Our Pledge
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We as members, contributors, and leaders pledge to make participation in our
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community a harassment-free experience for everyone, regardless of age, body
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size, visible or invisible disability, ethnicity, sex characteristics, gender
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identity and expression, level of experience, education, socio-economic status,
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nationality, personal appearance, race, caste, color, religion, or sexual
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identity and orientation.
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We pledge to act and interact in ways that contribute to an open, welcoming,
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diverse, inclusive, and healthy community.
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## Our Standards
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Examples of behavior that contributes to a positive environment for our
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community include:
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* Demonstrating empathy and kindness toward other people
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* Being respectful of differing opinions, viewpoints, and experiences
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* Giving and gracefully accepting constructive feedback
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* Accepting responsibility and apologizing to those affected by our mistakes,
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and learning from the experience
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* Focusing on what is best not just for us as individuals, but for the overall
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community
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Examples of unacceptable behavior include:
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* The use of sexualized language or imagery, and sexual attention or advances of
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any kind
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* Trolling, insulting or derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or email address,
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without their explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Enforcement Responsibilities
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Community leaders are responsible for clarifying and enforcing our standards of
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acceptable behavior and will take appropriate and fair corrective action in
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response to any behavior that they deem inappropriate, threatening, offensive,
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or harmful.
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Community leaders have the right and responsibility to remove, edit, or reject
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comments, commits, code, wiki edits, issues, and other contributions that are
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not aligned to this Code of Conduct, and will communicate reasons for moderation
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decisions when appropriate.
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## Scope
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This Code of Conduct applies within all community spaces, and also applies when
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an individual is officially representing the community in public spaces.
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Examples of representing our community include using an official e-mail address,
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posting via an official social media account, or acting as an appointed
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representative at an online or offline event.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported to the community leaders responsible for enforcement at
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[INSERT CONTACT METHOD].
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All complaints will be reviewed and investigated promptly and fairly.
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All community leaders are obligated to respect the privacy and security of the
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reporter of any incident.
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## Enforcement Guidelines
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Community leaders will follow these Community Impact Guidelines in determining
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the consequences for any action they deem in violation of this Code of Conduct:
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### 1. Correction
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**Community Impact**: Use of inappropriate language or other behavior deemed
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unprofessional or unwelcome in the community.
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**Consequence**: A private, written warning from community leaders, providing
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clarity around the nature of the violation and an explanation of why the
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behavior was inappropriate. A public apology may be requested.
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### 2. Warning
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**Community Impact**: A violation through a single incident or series of
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actions.
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**Consequence**: A warning with consequences for continued behavior. No
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interaction with the people involved, including unsolicited interaction with
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those enforcing the Code of Conduct, for a specified period of time. This
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includes avoiding interactions in community spaces as well as external channels
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like social media. Violating these terms may lead to a temporary or permanent
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ban.
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### 3. Temporary Ban
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**Community Impact**: A serious violation of community standards, including
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sustained inappropriate behavior.
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**Consequence**: A temporary ban from any sort of interaction or public
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communication with the community for a specified period of time. No public or
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private interaction with the people involved, including unsolicited interaction
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with those enforcing the Code of Conduct, is allowed during this period.
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Violating these terms may lead to a permanent ban.
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### 4. Permanent Ban
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**Community Impact**: Demonstrating a pattern of violation of community
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standards, including sustained inappropriate behavior, harassment of an
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individual, or aggression toward or disparagement of classes of individuals.
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**Consequence**: A permanent ban from any sort of public interaction within the
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community.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage],
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version 2.1, available at
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[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
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Community Impact Guidelines were inspired by
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[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
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For answers to common questions about this code of conduct, see the FAQ at
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[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
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[https://www.contributor-covenant.org/translations][translations].
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[homepage]: https://www.contributor-covenant.org
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[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
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[Mozilla CoC]: https://github.com/mozilla/diversity
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[FAQ]: https://www.contributor-covenant.org/faq
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[translations]: https://www.contributor-covenant.org/translations

‎CONTRIBUTING.md

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# Contributing to OpenProblems
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[OpenProblems](https://openproblems.bio) is a community effort, and
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everyone is welcome to contribute. This project is hosted on
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[github.com/openproblems-bio/openproblems](https://github.com/openproblems-bio/openproblems).
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You can find a full in depth guide on how to contribute to this project
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on the [OpenProblems website](https://openproblems.bio/documentation/).
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## Code of conduct
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We as members, contributors, and leaders pledge to make participation in
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our community a harassment-free experience for everyone, regardless of
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age, body size, visible or invisible disability, ethnicity, sex
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characteristics, gender identity and expression, level of experience,
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education, socio-economic status, nationality, personal appearance,
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race, caste, color, religion, or sexual identity and orientation.
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We pledge to act and interact in ways that contribute to an open,
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welcoming, diverse, inclusive, and healthy community.
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Our full [Code of Conduct](CODE_OF_CONDUCT.md) is adapted from the
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[Contributor Covenant](https://www.contributor-covenant.org), version
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2.1.

‎LICENSE

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MIT License
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Copyright (c) 2020 OpenProblems
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎README.md

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[![](https://openproblems.bio/images/heros/home_hero_text.png)](https://openproblems.bio)
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------
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Open Problems is a living, extensible, community-guided benchmarking platform.
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Useful links:
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* [Introduction to Open Problems](https://openproblems.bio)
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* [Our benchmarks](https://openproblems.bio/results)
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* [Our datasets](https://openproblems.bio/datasets)
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* [Our team and community](https://openproblems.bio/team)
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* [Planned and past events](https://openproblems.bio/events)
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* [How to contribute](https://openproblems.bio/documentation)

‎_viash.yaml

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viash_version: 0.8.6
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source: src
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target: target
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config_mods: |
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.functionality.version := 'dev'
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.platforms[.type == 'docker'].target_registry := 'ghcr.io'
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.platforms[.type == 'docker'].target_organization := 'openproblems-bio/openproblems'
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.platforms[.type == 'docker'].target_image_source := 'https://github.com/openproblems-bio/openproblems'
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.platforms[.type == "nextflow"].directives.tag := "$id"
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.platforms[.type == "nextflow"].auto.simplifyOutput := false
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.platforms[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", veryhightime : "time = 24.h" }
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.platforms[.type == "nextflow"].config.script := "process.errorStrategy = 'ignore'"

‎main.nf

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workflow {
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print("This is a dummy placeholder for pipeline execution. Please use the corresponding nf files for running pipelines.")
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}

‎nextflow.config

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process.container = 'nextflow/bash:latest'

‎scripts/sync_resources.sh

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#!/bin/bash
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set -e
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viash run src/common/sync_test_resources/config.vsh.yaml

‎src/common/check_dataset_schema/config.vsh.yaml

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functionality:
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name: check_dataset_schema
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namespace: common
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description: Checks if the dataset has the necessary slots that are predefined in a schema.
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argument_groups:
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- name: Inputs
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arguments:
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- name: --input
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type: file
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required: true
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description: A h5ad file.
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- name: --schema
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type: file
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required: true
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description: A schema file for the h5ad object.
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- name: Arguments
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arguments:
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- name: --stop_on_error
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type: boolean
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default: false
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description: Whether or not to stop with exit code 1 if the input file does not adhere to the schema.
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- name: Output
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arguments:
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- name: --output
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type: file
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required: true
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description: If specified, this file will contain a structured log of which checks succeeded (or not).
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example: checks.json
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direction: output
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resources:
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- type: python_script
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path: script.py
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test_resources:
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- path: /resources_test/common/pancreas
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- type: python_script
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path: test.py
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platforms:
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- type: docker
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image: openproblems/base_python:1.0.0
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test_setup:
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- type: python
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packages: viashpy
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- type: nextflow
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directives:
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label: [midtime, midmem, midcpu]

‎src/common/check_dataset_schema/script.py

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import anndata as ad
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import yaml
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import json
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## VIASH START
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par = {
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'input': 'work/d4/f4fabc8aa4f2308841d4ab57bcff62/_viash_par/input_1/dataset.h5ad',
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'schema': 'work/d4/f4fabc8aa4f2308841d4ab57bcff62/_viash_par/schema_1/schema.yaml',
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'stop_on_error': False,
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'output': 'work/d4/f4fabc8aa4f2308841d4ab57bcff62/out.yaml',
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}
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## VIASH END
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def check_structure(slot, slot_info, adata_slot):
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missing = []
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if slot == "X":
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slot_info["name"] = "X"
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slot_info = [slot_info]
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for obj in slot_info:
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adata_data = adata_slot.get(obj['name']) if slot != 'X' else adata_slot
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if obj.get('required') and adata_data is None:
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missing.append(obj['name'])
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# todo: check types
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return missing
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print('Load data', flush=True)
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adata = ad.read_h5ad(par['input'])
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# create data structure
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out = {
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"exit_code": 0,
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"error": {},
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"data_schema": "ok"
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}
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print("Check AnnData against schema", flush=True)
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with open(par["schema"], "r") as f:
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data_struct = yaml.safe_load(f)
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def_slots = data_struct['info']['slots']
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out = {
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"exit_code": 0,
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"error": {},
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"data_schema": "ok"
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}
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for slot in def_slots:
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print("Checking slot", slot, flush=True)
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missing = check_structure(slot, def_slots[slot], getattr(adata, slot))
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if missing:
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print(f"Dataset is missing {slot} {missing}", flush=True)
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out['exit_code'] = 1
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out['data_schema'] = 'not ok'
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out['error'][slot] = missing
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with open(par["output"], "w") as f:
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json.dump(out, f, indent=2)
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if par['stop_on_error']:
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exit(out['exit_code'])

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