Annotate repeats per family #1438
Workflow file for this run
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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] | |
| workflow_dispatch: | |
| env: | |
| NXF_ANSI_LOG: false | |
| NFTEST_VER: "0.9.2" | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| permissions: | |
| checks: write | |
| jobs: | |
| test: | |
| name: ${{ matrix.tags }} | ${{ matrix.profile }} | NF-${{ matrix.NXF_VER }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| - "24.04.2" | |
| - "latest-everything" | |
| tags: | |
| - "samplesheet" | |
| - "samplesheet_multisample_bam" | |
| - "samplesheet_multisample_ont_bam" | |
| - "SHORT_VARIANT_CALLING" | |
| - "SNV_ANNOTATION" | |
| - "CALL_SVS" | |
| - "ANNOTATE_SVS" | |
| - "RANK_VARIANTS" | |
| - "CALL_REPEAT_EXPANSIONS" | |
| - "METHYLATION" | |
| profile: | |
| - "docker" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Fetch ${{ github.event.pull_request.base.ref }} branch | |
| run: | | |
| git remote add upstream ${{ github.event.repository.clone_url }} | |
| git fetch upstream ${{ github.event.pull_request.base.ref }} | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - uses: nf-core/setup-nf-test@v1 | |
| with: | |
| version: ${{ env.NFTEST_VER }} | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| architecture: "x64" | |
| - name: Cache pdiff | |
| uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 | |
| id: cache-pip-pdiff | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-pdiff | |
| - name: Install pdiff | |
| run: python -m pip install --upgrade pip pdiff cryptography | |
| - name: Run nf-test | |
| run: | | |
| nf-test test \ | |
| --ci \ | |
| --changed-since upstream/${{ github.event.pull_request.base.ref }} \ | |
| --verbose \ | |
| --tag ${{ matrix.tags }} \ | |
| --profile "+${{ matrix.profile }}" \ | |
| --junitxml=test.xml |