update seqqc illumina test #17
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| name: BACPAQ Full Workflow CI | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| - master | |
| - github_actions_jl | |
| pull_request: | |
| workflow_dispatch: | |
| 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: "${{ github.event_name == 'push' || github.event_name == 'pull_request' || github.repository == 'cidgoh/bacpaq' }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| BACPAQ_TEST_CONFIG: | |
| - "test" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v3 | |
| - name: Set up pipeline pre-reqs | |
| run: | | |
| curl https://object-arbutus.cloud.computecanada.ca/cidgohshare/database/tar/adaptors.tar.gz -o adaptors.tar.gz | |
| tar -xzvf adaptors.tar.gz | |
| curl https://object-arbutus.cloud.computecanada.ca/cidgohshare/database/tar/busco_bacteria_odb10.tar.gz -o busco_bacteria_odb10.tar.gz | |
| tar -xzvf busco_bacteria_odb10.tar.gz | |
| curl https://object-arbutus.cloud.computecanada.ca/cidgohshare/database/tar/confindr.tar.gz -o confindr.tar.gz | |
| tar -xzvf confindr.tar.gz | |
| curl https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20240605.tar.gz -o k2_viral_20240605.tar.gz | |
| mkdir kraken2_db | |
| tar -xzvf k2_viral_20240605.tar.gz -C kraken2_db | |
| curl https://genome-idx.s3.amazonaws.com/centrifuge/p_compressed%2Bh%2Bv.tar.gz -o centrifuge.tar.gz | |
| mkdir centrifuge_db | |
| tar -xzvf centrifuge.tar.gz -C centrifuge_db | |
| mkdir bakta_db | |
| ls | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Run pipeline with test data | |
| # TODO nf-core: You can customise CI pipeline run tests as required | |
| # For example: adding multiple test runs with different parameters | |
| # Remember that you can parallelise this by using strategy.matrix | |
| run: | | |
| kraken2_db=./kraken2_db | |
| confindr_db=./confindr | |
| busco_db=./busco_bacteria_odb10 | |
| bakta_db=./bakta_db | |
| adaptors=./adaptors/test.fa | |
| nextflow run ${GITHUB_WORKSPACE} \ | |
| -profile ${{ matrix.BACPAQ_TEST_CONFIG }},docker \ | |
| --outdir ./results |