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Merge pull request #179 from qbic-pipelines/dev
Release 2.1
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‎.devcontainer/devcontainer.json

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{
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"name": "nfcore",
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"image": "nfcore/gitpod:latest",
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"remoteUser": "gitpod",
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// Configure tool-specific properties.
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"customizations": {
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// Configure properties specific to VS Code.
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"vscode": {
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// Set *default* container specific settings.json values on container create.
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"settings": {
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"python.defaultInterpreterPath": "/opt/conda/bin/python",
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"python.linting.enabled": true,
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"python.linting.pylintEnabled": true,
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"python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
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"python.formatting.yapfPath": "/opt/conda/bin/yapf",
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"python.linting.flake8Path": "/opt/conda/bin/flake8",
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"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
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"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
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"python.linting.pylintPath": "/opt/conda/bin/pylint"
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},
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// Add the IDs of extensions you want installed when the container is created.
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"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
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}
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}
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}

‎.editorconfig

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@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
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indent_size = 4
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indent_style = space
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[*.{md,yml,yaml,html,css,scss,js}]
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[*.{md,yml,yaml,html,css,scss,js,cff}]
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indent_size = 2
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# These files are edited and tested upstream in nf-core/modules

‎.gitattributes

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*.config linguist-language=nextflow
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*.nf.test linguist-language=nextflow
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modules/nf-core/** linguist-generated
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subworkflows/nf-core/** linguist-generated

‎.github/CONTRIBUTING.md

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@@ -52,9 +52,7 @@ These tests are run both with the latest available version of `Nextflow` and als
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## Getting help
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//TODO: Delete this completely? There is no slack to join!
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For further information/help, please consult the [nf-core/rnadeseq documentation](https://nf-co.re/rnadeseq/usage) and don't hesitate to get in touch on the nf-core Slack [#rnadeseq](https://nfcore.slack.com/channels/rnadeseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
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For further information/help, please consult the [qbic-pipelines/rnadeseq documentation](https://github.com/qbic-pipelines/rnadeseq/blob/master/docs/usage.md).
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## Pipeline contribution conventions
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‎.github/ISSUE_TEMPLATE/bug_report.yml

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attributes:
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label: System information
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description: |
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* Nextflow version _(eg. 21.10.3)_
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* Nextflow version _(eg. 22.10.1)_
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* Hardware _(eg. HPC, Desktop, Cloud)_
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* Executor _(eg. slurm, local, awsbatch)_
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* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_

‎.github/ISSUE_TEMPLATE/config.yml

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This file was deleted.

‎.github/workflows/ci.yml

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strategy:
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matrix:
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# Nextflow versions
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include:
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# Test pipeline minimum Nextflow version
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- NXF_VER: "21.10.3"
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NXF_EDGE: ""
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# Test latest edge release of Nextflow
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- NXF_VER: ""
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NXF_EDGE: "1"
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NXF_VER:
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- "22.10.1"
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- "latest-everything"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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environment.yml
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- name: Build new docker image
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if: env.MATCHED_FILES
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run: docker build --no-cache . -t qbicpipelines/rnadeseq:2.0.1
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run: docker build --no-cache . -t qbicpipelines/rnadeseq:2.1
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- name: Pull docker image
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if: ${{ !env.MATCHED_FILES }}
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run: |
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docker pull qbicpipelines/rnadeseq:dev
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docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:2.0.1
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docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:2.1
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- name: Install Nextflow
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env:
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NXF_VER: ${{ matrix.NXF_VER }}
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# Uncomment only if the edge release is more recent than the latest stable release
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# See https://github.com/nextflow-io/nextflow/issues/2467
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# NXF_EDGE: ${{ matrix.NXF_EDGE }}
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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uses: nf-core/setup-nextflow@v1
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with:
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version: "${{ matrix.NXF_VER }}"
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- name: Run pipeline with test data
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run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker
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name: Test workflow parameters
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runs-on: ubuntu-latest
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env:
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NXF_VER: "21.10.3"
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NXF_VER: "22.10.1"
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NXF_ANSI_LOG: false
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strategy:
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# This tells github to continue running other profile tests if some tests fail (default cancels all tests upon failure)
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fail-fast: false
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matrix:
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config:
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[
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"test",
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"test_full",
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"test_contrast_matrix",
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"test_contrast_list",
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"test_no_multiqc",
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"test_relevel",
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"test_skip_pathway_analysis",
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"test_star_rsem",
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"test_star_salmon",
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"test_use_vst",
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"test_batcheffect",
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"test_custom_gmt",
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]
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steps:
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- name: Check out pipeline code
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environment.yml
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- name: Build new docker image
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if: env.MATCHED_FILES
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run: docker build --no-cache . -t qbicpipelines/rnadeseq:2.0.1
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run: docker build --no-cache . -t qbicpipelines/rnadeseq:2.1
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- name: Pull docker image
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if: ${{ !env.MATCHED_FILES }}
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run: |
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docker pull qbicpipelines/rnadeseq:dev
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docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:2.0.1
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docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:2.1
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- name: Install Nextflow
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env:
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NXF_VER: ${{ matrix.NXF_VER }}
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# Uncomment only if the edge release is more recent than the latest stable release
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# See https://github.com/nextflow-io/nextflow/issues/2467
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# NXF_EDGE: ${{ matrix.NXF_EDGE }}
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uses: nf-core/setup-nextflow@v1
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with:
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version: "${{ matrix.NXF_VER }}"
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: "3.x"
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- name: Install dependencies
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run: python -m pip install --upgrade pip pytest-workflow
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- name: Run pipeline with tests settings
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uses: Wandalen/[email protected]
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with:
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command: pytest --tag ${{ matrix.config }} --kwdof --git-aware --color=yes
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attempt_limit: 3
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- name: Output log on failure
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if: failure()
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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sudo apt install bat > /dev/null
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batcat --decorations=always --color=always /tmp/pytest_workflow_*/*/log.{out,err}
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- name: Run pipeline with test data
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run: nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.config }},docker
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- name: Upload logs on failure
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if: failure()
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uses: actions/upload-artifact@v2
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with:
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name: logs-${{ matrix.profile }}
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path: |
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/tmp/pytest_workflow_*/*/.nextflow.log
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/tmp/pytest_workflow_*/*/log.out
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/tmp/pytest_workflow_*/*/log.err
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/tmp/pytest_workflow_*/*/work
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!/tmp/pytest_workflow_*/*/work/conda
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!/tmp/pytest_workflow_*/*/work/singularity
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/tmp/pytest_workflow_*/**/.command.log

‎.github/workflows/fix-linting.yml

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name: Fix linting from a comment
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on:
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issue_comment:
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types: [created]
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jobs:
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deploy:
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# Only run if comment is on a PR with the main repo, and if it contains the magic keywords
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if: >
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contains(github.event.comment.html_url, '/pull/') &&
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contains(github.event.comment.body, '@nf-core-bot fix linting') &&
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github.repository == 'nf-core/rnadeseq'
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runs-on: ubuntu-latest
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steps:
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# Use the @nf-core-bot token to check out so we can push later
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- uses: actions/checkout@v3
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with:
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token: ${{ secrets.nf_core_bot_auth_token }}
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# Action runs on the issue comment, so we don't get the PR by default
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# Use the gh cli to check out the PR
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- name: Checkout Pull Request
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run: gh pr checkout ${{ github.event.issue.number }}
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env:
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GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
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- uses: actions/setup-node@v3
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- name: Install Prettier
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run: npm install -g prettier @prettier/plugin-php
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# Check that we actually need to fix something
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- name: Run 'prettier --check'
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id: prettier_status
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run: |
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if prettier --check ${GITHUB_WORKSPACE}; then
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echo "name=result::pass" >> $GITHUB_OUTPUT
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else
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echo "name=result::fail" >> $GITHUB_OUTPUT
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fi
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- name: Run 'prettier --write'
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if: steps.prettier_status.outputs.result == 'fail'
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run: prettier --write ${GITHUB_WORKSPACE}
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- name: Commit & push changes
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if: steps.prettier_status.outputs.result == 'fail'
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run: |
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git config user.email "[email protected]"
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git config user.name "nf-core-bot"
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git config push.default upstream
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git add .
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git status
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git commit -m "[automated] Fix linting with Prettier"
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git push

‎.github/workflows/linting.yml

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# that the code meets the nf-core guidelines.
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on:
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push:
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branches:
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- dev
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pull_request:
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release:
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types: [published]
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EditorConfig:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v3
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- uses: actions/setup-node@v2
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- uses: actions/setup-node@v3
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- name: Install editorconfig-checker
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run: npm install -g editorconfig-checker
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Prettier:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v3
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- uses: actions/setup-node@v2
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- uses: actions/setup-node@v3
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- name: Install Prettier
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run: npm install -g prettier
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- name: Run Prettier --check
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run: prettier --check ${GITHUB_WORKSPACE}
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PythonBlack:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Check code lints with Black
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uses: psf/black@stable
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# If the above check failed, post a comment on the PR explaining the failure
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- name: Post PR comment
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if: failure()
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uses: mshick/add-pr-comment@v1
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with:
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message: |
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## Python linting (`black`) is failing
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To keep the code consistent with lots of contributors, we run automated code consistency checks.
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To fix this CI test, please run:
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* Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
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* Fix formatting errors in your pipeline: `black .`
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Once you push these changes the test should pass, and you can hide this comment :+1:
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We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
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Thanks again for your contribution!
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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allow-repeats: false
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nf-core:
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runs-on: ubuntu-latest
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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uses: actions/checkout@v3
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- name: Install Nextflow
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env:
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CAPSULE_LOG: none
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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uses: nf-core/setup-nextflow@v1
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- uses: actions/setup-python@v1
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- uses: actions/setup-python@v4
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with:
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python-version: "3.6"
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python-version: "3.7"
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architecture: "x64"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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- name: Upload linting log file artifact
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if: ${{ always() }}
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uses: actions/upload-artifact@v2
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uses: actions/upload-artifact@v3
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with:
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name: linting-logs
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path: |

‎.github/workflows/linting_comment.yml

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- name: Get PR number
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id: pr_number
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run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
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run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
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- name: Post PR comment
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uses: marocchino/sticky-pull-request-comment@v2

‎.gitignore

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data/
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results/
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.DS_Store
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tests/test_data
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*.pyc
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.Rhistory
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.RData
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testing/
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testing*
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*.pyc

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