sarek/.github/workflows/ci.yml at a6dc103abd912d444ee3b3df2bd5113c4ed19ad1 · FriederikeHanssen/sarek · GitHub

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name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
  push:
    branches:
      - dev
  pull_request:
  release:
    types: [published]

env:
  NXF_ANSI_LOG: false
  CAPSULE_LOG: none

jobs:
  test:
    name: Run pipeline with test data
    # Only run on push if this is the nf-core dev branch (merged PRs)
    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/sarek') }}"
    runs-on: ubuntu-latest
    strategy:
      # HACK Remove after DSL2 rewrite is done
      fail-fast: false
      matrix:
        # Nextflow versions
        include:
          # Test pipeline minimum Nextflow version
          - NXF_VER: "21.10.3"
            NXF_EDGE: ""
          # Test latest edge release of Nextflow
          - NXF_VER: ""
            NXF_EDGE: "1"
        test:
          - "aligner"
          - "annotation"
          - "cnvkit"
          - "controlfreec"
          - "deepvariant"
          - "default"
          - "freebayes"
          - "gatk4_spark"
          - "haplotypecaller"
          - "manta"
          - "markduplicates"
          - "mpileup"
          - "msisensorpro"
          - "mutect2"
          - "prepare_recalibration"
          - "recalibrate"
          - "save_bam_mapped"
          - "save_output_as_bam"
          - "skip_markduplicates"
          - "split_fastq"
          - "strelka"
          - "strelkabp"
          - "targeted"
          - "tiddit"
          - "trimming"
          - "tumor_normal_pair"
          - "variantcalling_channel"

    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v2

      - name: Install Nextflow
        env:
          NXF_VER: ${{ matrix.NXF_VER }}
          # Uncomment only if the edge release is more recent than the latest stable release
          # See https://github.com/nextflow-io/nextflow/issues/2467
          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
          nextflow self-update

      - name: Set up Python
        uses: actions/setup-python@v2
        with:
          python-version: "3.x"

      - name: Install dependencies
        run: python -m pip install --upgrade pip pytest-workflow

      - name: Run pipeline with tests settings
        uses: Wandalen/wretry.action@v1.0.11
        with:
          command: pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes
          attempt_limit: 3

      - name: Output log on failure
        if: failure()
        run: |
          sudo apt install bat > /dev/null
          batcat --decorations=always --color=always /tmp/pytest_workflow_*/*/log.{out,err}

      - name: Upload logs on failure
        if: failure()
        uses: actions/upload-artifact@v2
        with:
          name: logs-${{ matrix.profile }}
          path: |
            /tmp/pytest_workflow_*/*/.nextflow.log
            /tmp/pytest_workflow_*/*/log.out
            /tmp/pytest_workflow_*/*/log.err
            /tmp/pytest_workflow_*/*/work
            !/tmp/pytest_workflow_*/*/work/conda
            !/tmp/pytest_workflow_*/*/work/singularity
            /tmp/pytest_workflow_*/**/.command.log