fix: Replace deprecated docker.userEmulation with equivalent docker.r… #130
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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: | |
| - develop | |
| pull_request: | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| env: | |
| NXF_ANSI_LOG: false | |
| jobs: | |
| test: | |
| name: Run pipeline with test data | |
| # Only run on push if this is the develop branch (merged PRs) | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'ksumngs/yavsap') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "21.10.3" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Run pipeline with test data | |
| env: | |
| NCBI_API_KEY: ${{ secrets.NCBI_API_KEY }} | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,gh,docker --outdir results | |
| parameters: | |
| name: Test workflow parameters | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'ksumngs/yavsap') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| parameters: | |
| - "--keep_taxid classified" | |
| - "--kraken2_db https://genome-idx.s3.amazonaws.com/kraken/16S_Silva132_20200326.tgz --keep_taxid unclassified" | |
| - "--kraken2_db ~/kraken2-db" | |
| - "--genome_list ./genomes/jev.tsv" | |
| - "--genome_list jev" | |
| - "--skip_qc" | |
| - "--skip_trimming" | |
| - "--skip_filtering" | |
| - "--skip_haplotype" | |
| - "--skip_phylogenetics" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| - name: Download Kraken2 database | |
| if: ${{ matrix.parameters == '--kraken2_db ~/kraken2-db' }} | |
| run: | | |
| mkdir ~/kraken2-db | |
| wget -qO- https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20210517.tar.gz | tar xzv -C ~/kraken2-db | |
| - name: Run pipeline with test data | |
| env: | |
| NCBI_API_KEY: ${{ secrets.NCBI_API_KEY }} | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,gh,docker ${{ matrix.parameters }} --outdir results | |
| test_interleaved: | |
| name: Test Interleaved Reads Workflow | |
| # Only run on push if this is the develop branch (merged PRs) | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'ksumngs/yavsap') }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| - name: Run pipeline with test data | |
| env: | |
| NCBI_API_KEY: ${{ secrets.NCBI_API_KEY }} | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_interleaved,gh,docker --outdir results | |
| test_nanopore: | |
| name: Run workflow tests | |
| # Only run on push if this is the develop branch (merged PRs) | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'ksumngs/yavsap') }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| - name: Run pipeline with test data | |
| env: | |
| NCBI_API_KEY: ${{ secrets.NCBI_API_KEY }} | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,gh,docker --outdir results |