fix cardinality when params.bowtie2_index used #1336
Workflow file for this run
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: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Free some space | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| - name: Free Disk Space (Ubuntu) | |
| uses: jlumbroso/[email protected] | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ 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 --publish_dir_mode link --outdir ./results | |
| parameters: | |
| name: Test workflow parameters | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| parameters: | |
| - "--consensus_caller ivar" | |
| - "--variant_caller bcftools --consensus_caller ivar" | |
| - "--skip_fastp --skip_pangolin" | |
| - "--skip_variants" | |
| - "--skip_cutadapt --skip_snpeff" | |
| - "--skip_kraken2" | |
| - "--skip_assembly" | |
| - "--spades_mode corona" | |
| - "--spades_mode metaviral" | |
| - "--skip_plasmidid false --skip_asciigenome" | |
| - "--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Free some space | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| - name: Free Disk Space (Ubuntu) | |
| uses: jlumbroso/[email protected] | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Download GTF for additional annotation | |
| if: contains(matrix.parameters, 'additional_annotation') | |
| run: | | |
| wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3/GCA_009858895.3_ASM985889v3_genomic.gtf.gz | |
| - name: Run pipeline with various parameters | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }} --publish_dir_mode link --outdir ./results | |
| test_sispa: | |
| name: Test SISPA workflow | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| parameters: | |
| - "--gff false" | |
| - "--genome 'NC_045512.2'" | |
| 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 minimal SISPA data and various options | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_sispa,docker ${{ matrix.parameters }} --outdir ./results | |
| test_nanopore: | |
| name: Test Nanopore workflow | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| parameters: | |
| - "--gff false --freyja_depthcutoff 1" | |
| - "--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz --freyja_depthcutoff 1" | |
| - "--input false --freyja_depthcutoff 1" | |
| - "--min_barcode_reads 10000" | |
| - "--min_guppyplex_reads 10000" | |
| - "--artic_minion_caller medaka --sequencing_summary false --fast5_dir false --freyja_depthcutoff 1" | |
| - "--artic_minion_caller medaka --sequencing_summary false --fast5_dir false --artic_minion_medaka_model ./r941_min_high_g360_model.hdf5 --freyja_depthcutoff 1" | |
| 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: Download GTF for additional annotation | |
| if: contains(matrix.parameters, 'additional_annotation') | |
| run: | | |
| wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3/GCA_009858895.3_ASM985889v3_genomic.gtf.gz | |
| - name: Download medaka model | |
| if: contains(matrix.parameters, 'r941_min_high_g360_model.hdf5') | |
| run: | | |
| wget https://github.com/nanoporetech/medaka/raw/master/medaka/data/r941_min_high_g360_model.hdf5 | |
| - name: Run pipeline with minimal Nanopore data and various options | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_nanopore,docker ${{ matrix.parameters }} --outdir ./results |