add hic minimap2 #407
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] | |
| env: | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| SINGULARITY_DISABLE_CACHE: true | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Run pipeline with test data | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'sanger-tol/genomeassembly') }}" | |
| runs-on: ubuntu2204-4c | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "22.10.1" | |
| - "latest-everything" | |
| steps: | |
| - name: Login to GitHub Container Registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Set up nextflow secrets | |
| run: | | |
| nextflow secrets set NCBI_API_KEY ${{ secrets.NCBI_API_KEY }} | |
| - name: Download test data | |
| run: | | |
| curl https://tolit.cog.sanger.ac.uk/test-data/resources/genomeassembly/genomeassembly_test_data.tar.gz | tar xzf - | |
| - name: Setup apptainer | |
| uses: eWaterCycle/setup-apptainer@main | |
| - name: Set up Singularity | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| - name: Run pipeline with test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_github,singularity --outdir ./results |