mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
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'
|
|
|
|
process VCF2MAF {
|
|
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::vcf2maf=1.6.21 bioconda::ensembl-vep=106.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0':
|
|
'quay.io/biocontainers/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(vcf) // Use an uncompressed VCF file!
|
|
path fasta // Required
|
|
path vep_cache // Required for VEP running. A default of /.vep is supplied.
|
|
|
|
output:
|
|
tuple val(meta), path("*.maf"), emit: maf
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
def vep_cache_cmd = vep_cache ? "--vep-data $vep_cache" : ""
|
|
|
|
// If VEP is present, it will find it and add it to commands.
|
|
// If VEP is not present they will be blank
|
|
"""
|
|
if command -v vep &> /dev/null
|
|
then
|
|
VEP_CMD="--vep-path \$(dirname \$(type -p vep))"
|
|
VEP_VERSION=\$(echo -e "\\n ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')")
|
|
else
|
|
VEP_CMD=""
|
|
VEP_VERSION=""
|
|
fi
|
|
|
|
vcf2maf.pl \\
|
|
$args \\
|
|
\$VEP_CMD \\
|
|
$vep_cache_cmd \\
|
|
--ref-fasta $fasta \\
|
|
--input-vcf $vcf \\
|
|
--output-maf ${prefix}.maf
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
vcf2maf: $VERSION\$VEP_VERSION
|
|
END_VERSIONS
|
|
"""
|
|
}
|