Update nextclade & pangolin modules #1352
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] | |
| workflow_dispatch: | |
| env: | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})" | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "24.04.2" | |
| - "latest-everything" | |
| profile: | |
| - "conda" | |
| - "docker" | |
| - "singularity" | |
| test_name: | |
| - "test" | |
| isMaster: | |
| - ${{ github.base_ref == 'master' }} | |
| # Exclude conda and singularity on dev | |
| exclude: | |
| - isMaster: false | |
| profile: "conda" | |
| - isMaster: false | |
| profile: "singularity" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Set up Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Set up Apptainer | |
| if: matrix.profile == 'singularity' | |
| uses: eWaterCycle/setup-apptainer@main | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| - name: Set up Miniconda | |
| if: matrix.profile == 'conda' | |
| uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| conda-solver: libmamba | |
| channels: conda-forge,bioconda | |
| - name: Set up Conda | |
| if: matrix.profile == 'conda' | |
| run: | | |
| echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | |
| echo $(realpath python) >> $GITHUB_PATH | |
| - name: Clean up Disk space | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results | |
| test_parameters: | |
| name: "Test parameters (${{ matrix.NXF_VER }} | ${{ matrix.parameters }} | ${{ matrix.profile }})" | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "24.04.2" | |
| - "latest-everything" | |
| profile: | |
| - "conda" | |
| - "docker" | |
| - "singularity" | |
| 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" | |
| - "--bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz" | |
| - "--skip_noninternal_primers --threeprime_adapters" | |
| isMaster: | |
| - ${{ github.base_ref == 'master' }} | |
| # Exclude conda and singularity on dev | |
| exclude: | |
| - isMaster: false | |
| profile: "conda" | |
| - isMaster: false | |
| profile: "singularity" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Set up Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Set up Apptainer | |
| if: matrix.profile == 'singularity' | |
| uses: eWaterCycle/setup-apptainer@main | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| - name: Set up Miniconda | |
| if: matrix.profile == 'conda' | |
| uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| conda-solver: libmamba | |
| channels: conda-forge,bioconda | |
| - name: Set up Conda | |
| if: matrix.profile == 'conda' | |
| run: | | |
| echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | |
| echo $(realpath python) >> $GITHUB_PATH | |
| - name: Clean up Disk space | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - 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 prebuild bowtie2 index | |
| if: contains(matrix.parameters, 'bowtie2_index') | |
| run: | | |
| wget https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz | |
| - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.parameters }} | ${{ matrix.profile }}" | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,${{ matrix.profile }} ${{ matrix.parameters }} --outdir ./results | |
| test_sispa: | |
| name: "Test SISPA (${{ matrix.NXF_VER }} | ${{ matrix.parameters }} | ${{ matrix.profile }})" | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "24.04.2" | |
| - "latest-everything" | |
| profile: | |
| - "conda" | |
| - "docker" | |
| - "singularity" | |
| parameters: | |
| - "--gff false" | |
| - "--genome 'NC_045512.2'" | |
| isMaster: | |
| - ${{ github.base_ref == 'master' }} | |
| # Exclude conda and singularity on dev | |
| exclude: | |
| - isMaster: false | |
| profile: "conda" | |
| - isMaster: false | |
| profile: "singularity" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Set up Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Set up Apptainer | |
| if: matrix.profile == 'singularity' | |
| uses: eWaterCycle/setup-apptainer@main | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| - name: Set up Miniconda | |
| if: matrix.profile == 'conda' | |
| uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| conda-solver: libmamba | |
| channels: conda-forge,bioconda | |
| - name: Set up Conda | |
| if: matrix.profile == 'conda' | |
| run: | | |
| echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | |
| echo $(realpath python) >> $GITHUB_PATH | |
| - name: Clean up Disk space | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.parameters }} | ${{ matrix.profile }}" | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_sispa,${{ matrix.profile }} ${{ matrix.parameters }} --outdir ./results | |
| test_nanopore: | |
| name: "Test nanopore (${{ matrix.NXF_VER }} | ${{ matrix.parameters }} | ${{ matrix.profile }})" | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralrecon') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "24.04.2" | |
| - "latest-everything" | |
| profile: | |
| - "conda" | |
| - "docker" | |
| - "singularity" | |
| 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" | |
| isMaster: | |
| - ${{ github.base_ref == 'master' }} | |
| # Exclude conda and singularity on dev | |
| exclude: | |
| - isMaster: false | |
| profile: "conda" | |
| - isMaster: false | |
| profile: "singularity" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Set up Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Set up Apptainer | |
| if: matrix.profile == 'singularity' | |
| uses: eWaterCycle/setup-apptainer@main | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| - name: Set up Miniconda | |
| if: matrix.profile == 'conda' | |
| uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| conda-solver: libmamba | |
| channels: conda-forge,bioconda | |
| - name: Set up Conda | |
| if: matrix.profile == 'conda' | |
| run: | | |
| echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | |
| echo $(realpath python) >> $GITHUB_PATH | |
| - name: Clean up Disk space | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - 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 test data ${{ matrix.NXF_VER }} | ${{ matrix.parameters }} | ${{ matrix.profile }}" | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_nanopore,${{ matrix.profile }} ${{ matrix.parameters }} --outdir ./results |