Add bwa #45
Workflow file for this run
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| name: dry run CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| - dev | |
| env: | |
| NXF_ANSI_LOG: false | |
| jobs: | |
| test: | |
| name: Dry run ${{ matrix.inputtype }}-${{ matrix.profile }}-nf_${{ matrix.NXF_VER }} pipeline test | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.1" | |
| - "latest" | |
| inputtype: | |
| - fasta | |
| - illumina | |
| - nanopore | |
| profile: ["docker", "conda"] # TODO "singularity"] | |
| python-version: | |
| - "3.9" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v4 | |
| - uses: actions/cache@v4 | |
| with: | |
| path: /usr/local/bin/nextflow | |
| key: ${{ runner.os }} | |
| restore-keys: | | |
| ${{ runner.os }}-nextflow- | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Install nf-test | |
| run: | | |
| wget -qO- https://code.askimed.com/install/nf-test | bash | |
| sudo mv nf-test /usr/local/bin/ | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.7.1 | |
| - name: Set up miniconda | |
| if: matrix.profile == 'conda' | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| conda-solver: libmamba | |
| channels: conda-forge,bioconda,defaults | |
| python-version: ${{ matrix.python-version }} | |
| - name: Run nf-test | |
| run: nf-test test --profile=${{ matrix.profile }} tests/${{ matrix.inputtype }}/*.nf.test --tap=test.tap | |
| - uses: pcolby/tap-summary@v1 | |
| with: | |
| path: >- | |
| test.tap |