mirror of
https://github.com/MillironX/nf-core_modules.git
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2af071ed0d
* ci: Remove pytest_subworkflows * ci(bam_sort_samtools): Depend on paths-filter instead of pytest-workflow Co-authored-by: Harshil Patel <drpatelhh@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * ci: Revert back to one job branch * ci(align_bowtie2): Run tests that depend on bam_sort_samtools * ci: Fix anchor not being created yet * ci: Update sra_fastq tags and pytest_modules * fix(bam_sort_samtools): Update nextflow.config with params * test(subworkflows): Update gatk_create_som_pon tags * ci: Point to subworkflow_hacks branch of nf-core tools Co-authored-by: Harshil Patel <drpatelhh@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
107 lines
3.1 KiB
YAML
107 lines
3.1 KiB
YAML
name: Pytest-workflow
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on:
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push:
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branches: [master]
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pull_request:
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branches: [master]
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jobs:
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changes:
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name: Check for changes
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runs-on: ubuntu-latest
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outputs:
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# Expose matched filters as job 'modules' output variable
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modules: ${{ steps.filter.outputs.changes }}
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steps:
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- uses: actions/checkout@v2
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- uses: dorny/paths-filter@v2
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id: filter
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with:
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filters: "tests/config/pytest_modules.yml"
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test:
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runs-on: ubuntu-20.04
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name: ${{ matrix.tags }} ${{ matrix.profile }} ${{ matrix.nxf_version }}
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needs: changes
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if: needs.changes.outputs.modules != '[]'
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strategy:
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fail-fast: false
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matrix:
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nxf_version: ["21.04.0"]
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tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
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profile: ["docker", "singularity", "conda"]
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env:
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NXF_ANSI_LOG: false
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steps:
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- uses: actions/checkout@v2
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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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- uses: actions/cache@v2
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
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restore-keys: |
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${{ runner.os }}-pip-
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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 Python dependencies
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run: python -m pip install --upgrade pip pytest-workflow
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- uses: actions/cache@v2
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with:
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path: /usr/local/bin/nextflow
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key: ${{ runner.os }}-nextflow-${{ matrix.nxf_version }}
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restore-keys: |
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${{ runner.os }}-nextflow-
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- name: Install Nextflow
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env:
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NXF_VER: ${{ matrix.nxf_version }}
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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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- name: Set up Singularity
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if: matrix.profile == 'singularity'
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uses: eWaterCycle/setup-singularity@v5
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with:
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singularity-version: 3.7.1
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- name: Setup miniconda
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if: matrix.profile == 'conda'
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uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true
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channels: conda-forge,bioconda,defaults
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python-version: ${{ matrix.python-version }}
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- name: Conda clean
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if: matrix.profile == 'conda'
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run: conda clean -a
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# Test the module
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- name: Run pytest-workflow
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# only use one thread for pytest-workflow to avoid race condition on conda cache.
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run: NF_CORE_MODULES_TEST=1 TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof
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- name: Upload logs on failure
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if: failure()
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uses: actions/upload-artifact@v2
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with:
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name: logs-${{ matrix.profile }}-${{ matrix.nxf_version }}
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path: |
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/home/runner/pytest_workflow_*/*/.nextflow.log
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/home/runner/pytest_workflow_*/*/log.out
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/home/runner/pytest_workflow_*/*/log.err
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/home/runner/pytest_workflow_*/*/work
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