Add streptococcus workflow #256
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| name: CI | |
| # This workflow runs the pipeline with the minimal test dataset to check that | |
| # it completes without any syntax errors | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - dev | |
| pull_request: | |
| branches: | |
| - master | |
| - dev | |
| env: | |
| NXF_ANSI_LOG: false | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Install JASEN and run self-test pipeline | |
| # Only run on push if this is in the main repository | |
| if: "${{ github.repository == 'genomic-medicine-sweden/jasen' }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.10.1" | |
| organism: | |
| - "staphylococcus_aureus" | |
| #- "mycobacterium_tuberculosis" | |
| #- "klebsiella_pneumoniae" | |
| #- "escherichia_coli" | |
| steps: | |
| - name: Install Nextflow | |
| # For running (locally) with ACT, we use a docker image with Nextflow pre-installed | |
| if: "${{ ! github.event.act }}" | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Check-out git submodules | |
| # This should be done early so we can catch troubles with it early | |
| run: | | |
| cd ${GITHUB_WORKSPACE} && make check-and-reinit-git-submodules | |
| - name: Install Singularity | |
| # For running (locally) with ACT, we use a docker image with Singularity already installed | |
| if: "${{ ! github.event.act }}" | |
| run: | | |
| wget https://github.com/apptainer/singularity/releases/download/v3.8.7/singularity-container_3.8.7_amd64.deb && sudo dpkg -i singularity-container_3.8.7_amd64.deb | |
| - name: Install containers | |
| run: | |
| cd ${GITHUB_WORKSPACE}/container && sudo make build_local_containers && make download_remote_containers | |
| - name: Report disk-usage after building containers | |
| run: | |
| df -h | |
| - name: Run Make install only for S. Aureus | |
| run: | |
| make update_databases && df -h && make ${{ matrix.organism }}_all | |
| - name: Report disk-usage after S. Aureus part | |
| run: | |
| df -h | |
| - name: Adapt paths in samplelist.csv | |
| # We have to use '#' as a separator, as there are slashes in the $PWD | |
| # path, messing up with the s///-replace syntax | |
| run: | | |
| sed -i "s#PATH_TO_JASEN#$PWD#g" assets/test_data/samplelist.csv | |
| - name: Run pipeline with test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE}/main.nf -profile ${{ matrix.organism }} -config configs/nextflow.ci.config --csv assets/test_data/samplelist.csv |