New ivar_variants_to_vcf.py #183
Workflow file for this run
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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] | |
| 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: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Free some space | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| - name: Free Disk Space (Ubuntu) | |
| uses: jlumbroso/free-disk-space@v1.3.1 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ 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/free-disk-space@v1.3.1 | |
| - 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 |