Merge pull request #1226 from nf-core/bbsplit_no_overwrite #1
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Run pipeline with test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results | |
| star_salmon: | |
| name: Test STAR Salmon with workflow parameters | |
| if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| parameters: | |
| - "--skip_qc" | |
| - "--skip_trimming" | |
| - "--gtf false" | |
| - "--star_index false" | |
| - "--transcript_fasta false" | |
| - "--min_mapped_reads 90" | |
| - "--with_umi" | |
| - "--with_umi --skip_trimming" | |
| - "--remove_ribo_rna --skip_qualimap" | |
| - "--bam_csi_index" | |
| - "--save_align_intermeds --save_reference" | |
| - "--featurecounts_group_type false" | |
| - "--trimmer fastp" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline with STAR and various parameters | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results | |
| star_rsem: | |
| name: Test STAR RSEM with workflow parameters | |
| if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| parameters: | |
| - "--skip_qc" | |
| - "--rsem_index false" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline with RSEM STAR and various parameters | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results | |
| hisat2: | |
| name: Test HISAT2 with workflow parameters | |
| if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| parameters: | |
| - "--skip_qc" | |
| - "--hisat2_index false" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline with HISAT2 and various parameters | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results | |
| pseudo: | |
| name: Test Pseudoaligners with workflow parameters | |
| if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| parameters: | |
| - "--pseudo_aligner salmon --skip_qc" | |
| - "--pseudo_aligner salmon --skip_alignment --skip_pseudo_alignment" | |
| - "--pseudo_aligner salmon --salmon_index false --transcript_fasta false" | |
| - "--pseudo_aligner kallisto --skip_qc" | |
| - "--pseudo_aligner kallisto --skip_alignment --skip_pseudo_alignment" | |
| - "--pseudo_aligner kallisto --kallisto_index false --transcript_fasta false" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline with Salmon or Kallisto and various parameters | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }} --outdir ./results |