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vcf2maf module with built in VEP (#1768)
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
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7 changed files with 168 additions and 1 deletions
55
modules/vcf2maf/main.nf
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55
modules/vcf2maf/main.nf
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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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47
modules/vcf2maf/meta.yml
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modules/vcf2maf/meta.yml
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name: "vcf2maf"
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description: vcf2maf
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keywords:
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- "vcf2maf"
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- annotation
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tools:
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- "vcf2maf":
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description: |
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"Convert a VCF into a MAF where each variant is annotated to only one of all possible gene isoforms using vcf2maf. vcf2maf is designed to work with VEP, so it is recommended to have VEP and vcf2maf installed when running this module. Running VEP requires a VEP cache to be present. It is recommended to set the --species and --ncbi-build in ext.args (use the module config). If you wish to skip VEP, add `--inhibit-vep` to ext.args. It may also be necessary to set --tumor-id and --normal-id for correct parsing of the VCF."
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homepage: "https://github.com/mskcc/vcf2maf"
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documentation: "https://github.com/mskcc/vcf2maf"
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tool_dev_url: "https://github.com/mskcc/vcf2maf"
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doi: "10.5281/zenodo.593251"
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licence: "['Apache-2.0']"
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- vcf:
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type: file
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description: |
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vcf to convert to MAF format. Must be uncompressed.
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- vep_cache:
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type: file
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description: |
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Path to VEP cache dir. Required for correct running of VEP.
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- maf:
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type: file
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description: MAF file produced from VCF
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pattern: "*.maf"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@adamrtalbot"
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@ -2144,6 +2144,10 @@ vcf2db:
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- modules/vcf2db/**
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- modules/vcf2db/**
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- tests/modules/vcf2db/**
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- tests/modules/vcf2db/**
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vcf2maf:
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- modules/vcf2maf/**
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- tests/modules/vcf2maf/**
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vcfanno:
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vcfanno:
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- modules/vcfanno/**
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- modules/vcfanno/**
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- tests/modules/vcfanno/**
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- tests/modules/vcfanno/**
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@ -186,6 +186,8 @@ params {
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vcfanno_tar_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno_grch38_module_test.tar.gz"
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vcfanno_tar_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno_grch38_module_test.tar.gz"
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vcfanno_toml = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml"
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vcfanno_toml = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml"
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vep_cache = "${test_data_dir}/genomics/homo_sapiens/genome/vep.tar.gz"
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}
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}
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'pangenome' {
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'pangenome' {
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pangenome_fa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa"
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pangenome_fa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa"
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@ -234,7 +236,7 @@ params {
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mitochon_standin_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam"
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mitochon_standin_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam"
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mitochon_standin_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai"
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mitochon_standin_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai"
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test3_single_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam"
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test3_single_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam"
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read_group_settings_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/read_group_settings.txt"
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read_group_settings_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/read_group_settings.txt"
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30
tests/modules/vcf2maf/main.nf
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tests/modules/vcf2maf/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { VCF2MAF } from '../../../modules/vcf2maf/main.nf'
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include { UNTAR } from '../../../modules/untar/main.nf'
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workflow test_vcf2maf_no_vep {
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input_vcf = [
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[ id:'test' ],
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
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]
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fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
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VCF2MAF ( input_vcf, fasta, [] )
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}
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workflow test_vcf2maf_vep {
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input_vcf = [
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[ id:'test' ],
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
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]
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fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
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vep_cache = [ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['vep_cache'], checkIfExists: true) ]
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vep_cache_unpacked = UNTAR(vep_cache).untar.map { it[1] }
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VCF2MAF ( input_vcf, fasta, vep_cache_unpacked)
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}
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14
tests/modules/vcf2maf/nextflow.config
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tests/modules/vcf2maf/nextflow.config
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params.species = "homo_sapiens"
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params.build = "GRCh38"
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName: 'test_vcf2maf_no_vep:VCF2MAF' {
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ext.args = "--ncbi-build ${params.build} --species ${params.species} --inhibit-vep"
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container = "quay.io/biocontainers/vcf2maf:1.6.21--hdfd78af_0"
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}
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withName: 'test_vcf2maf_vep:VCF2MAF' {
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ext.args = "--ncbi-build ${params.build} --species ${params.species}"
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}
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}
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15
tests/modules/vcf2maf/test.yml
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tests/modules/vcf2maf/test.yml
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- name: vcf2maf test_vcf2maf_no_vep
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command: nextflow run ./tests/modules/vcf2maf -entry test_vcf2maf_no_vep -c ./tests/config/nextflow.config -c ./tests/modules/vcf2maf/nextflow.config
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tags:
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- vcf2maf
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files:
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- path: output/vcf2maf/test.maf
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md5sum: c7f357efa774fd5c4003d84f05212ed0
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- name: vcf2maf test_vcf2maf_vep
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command: nextflow run ./tests/modules/vcf2maf -entry test_vcf2maf_vep -c ./tests/config/nextflow.config -c ./tests/modules/vcf2maf/nextflow.config
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tags:
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- vcf2maf
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files:
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- path: output/vcf2maf/test.maf
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md5sum: bf114692a2f421225926c9b651eff161
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