Remove old workflow. Update PGEcore. Add more tools to workflow #156
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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 | |
| # NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| # NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| # concurrency: | |
| # group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| # cancel-in-progress: true | |
| # jobs: | |
| # test: | |
| # name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})" | |
| # # Only run on push if this is the nf-core dev branch (merged PRs) | |
| # if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/plasmodiumdrugres') }}" | |
| # runs-on: ubuntu-latest | |
| # strategy: | |
| # matrix: | |
| # NXF_VER: | |
| # - "24.04.2" | |
| # - "latest-everything" | |
| # profile: | |
| # - "conda" | |
| # - "docker" | |
| # - "singularity" | |
| # test_name: | |
| # - "test" | |
| # isMaster: | |
| # - ${{ github.base_ref == 'master' }} | |
| # # Exclude conda and singularity on dev | |
| # exclude: | |
| # - isMaster: false | |
| # profile: "conda" | |
| # - isMaster: false | |
| # profile: "singularity" | |
| # steps: | |
| # - name: Check out pipeline code | |
| # uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| # - name: Set up Nextflow | |
| # uses: nf-core/setup-nextflow@v2 | |
| # with: | |
| # version: "${{ matrix.NXF_VER }}" | |
| # - name: Set up Apptainer | |
| # if: matrix.profile == 'singularity' | |
| # uses: eWaterCycle/setup-apptainer@main | |
| # - name: Set up Singularity | |
| # if: matrix.profile == 'singularity' | |
| # run: | | |
| # mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| # mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| # - name: Set up Miniconda | |
| # if: matrix.profile == 'conda' | |
| # uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | |
| # with: | |
| # miniconda-version: "latest" | |
| # auto-update-conda: true | |
| # conda-solver: libmamba | |
| # channels: conda-forge,bioconda | |
| # - name: Set up Conda | |
| # if: matrix.profile == 'conda' | |
| # run: | | |
| # echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | |
| # echo $(realpath python) >> $GITHUB_PATH | |
| # - name: Clean up Disk space | |
| # uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| # - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" | |
| # run: | | |
| # nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results |