Merge pull request #407 from nf-core/exchange_qualimap_with_mosdepth #1005
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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 | |
| 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: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnafusion') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Dry test arriba build | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub --build_references \ | |
| --outdir /home/runner/work/rnafusion/rnafusion/results --arriba \ | |
| --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ | |
| --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} | |
| - name: Dry test arriba | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub \ | |
| --outdir /home/runner/work/rnafusion/rnafusion/results --arriba \ | |
| --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ | |
| --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} | |
| - name: Dry test squid build | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub --build_references \ | |
| --outdir /home/runner/work/rnafusion/rnafusion/results --squid \ | |
| --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ | |
| --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} | |
| - name: Dry test squid | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub \ | |
| --outdir /home/runner/work/rnafusion/rnafusion/results --squid \ | |
| --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ | |
| --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} | |
| - name: Dry test pizzly build | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub --build_references \ | |
| --outdir /home/runner/work/rnafusion/rnafusion/results --pizzly \ | |
| --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ | |
| --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} | |
| - name: Dry test pizzly | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub \ | |
| --outdir /home/runner/work/rnafusion/rnafusion/results --pizzly \ | |
| --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ | |
| --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} | |
| - name: Dry test fusioncatcher build | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub --build_references \ | |
| --outdir /home/runner/work/rnafusion/rnafusion/results --fusioncatcher \ | |
| --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ | |
| --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} | |
| - name: Dry test fusioncatcher | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub \ | |
| --outdir /home/runner/work/rnafusion/rnafusion/results --fusioncatcher \ | |
| --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ | |
| --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} | |
| - name: Dry test starfusion build | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub build_references \ | |
| --outdir /home/runner/work/rnafusion/rnafusion/results --starfusion \ | |
| --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ | |
| --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} | |
| - name: Dry test starfusion | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub \ | |
| --outdir /home/runner/work/rnafusion/rnafusion/results --starfusion \ | |
| --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ | |
| --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} | |
| - name: Dry test stingtie | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub \ | |
| --outdir /home/runner/work/rnafusion/rnafusion/results --stringtie \ | |
| --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ | |
| --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} |