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https://github.com/MillironX/nf-core_modules.git
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f19ec865aa
vcf2maf module created Additions: - vcf2maf module created - If VEP is present in PATH, it is added to command - If VEP is missing, it is ignored (recommended to skip with --inhibit-vep) - VEP version automatically added to versions.yml - Uses VEP cache during testing which is added to test-datasets in https://github.com/nf-core/test-datasets/pull/563 - Default Docker image includes VEP and vcf2maf - Test includes without VEP. Relates to #490
55 lines
1.8 KiB
Text
55 lines
1.8 KiB
Text
def VERSION = '1.6.21'
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process VCF2MAF {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::vcf2maf=1.6.21 bioconda::ensembl-vep=106.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0':
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'quay.io/biocontainers/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0' }"
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input:
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tuple val(meta), path(vcf) // Use an uncompressed VCF file!
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path fasta // Required
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path vep_cache // Required for VEP running. A default of /.vep is supplied.
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output:
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tuple val(meta), path("*.maf"), emit: maf
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def vep_cache_cmd = vep_cache ? "--vep-data $vep_cache" : ""
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// If VEP is present, it will find it and add it to commands.
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// If VEP is not present they will be blank
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"""
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if command -v vep &> /dev/null
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then
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VEP_CMD="--vep-path \$(dirname \$(type -p vep))"
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VEP_VERSION=\$(echo -e "\\n ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')")
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else
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VEP_CMD=""
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VEP_VERSION=""
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fi
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vcf2maf.pl \\
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$args \\
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\$VEP_CMD \\
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$vep_cache_cmd \\
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--ref-fasta $fasta \\
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--input-vcf $vcf \\
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--output-maf ${prefix}.maf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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vcf2maf: $VERSION\$VEP_VERSION
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END_VERSIONS
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"""
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}
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