mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 21:53:10 +00:00
46 lines
1.3 KiB
Text
46 lines
1.3 KiB
Text
|
process SVTK_STANDARDIZE {
|
||
|
|
tag "$meta.id"
|
||
|
|
label 'process_low'
|
||
|
|
|
||
|
|
conda (params.enable_conda ? "bioconda::svtk=0.0.20190615" : null)
|
||
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||
|
|
'https://depot.galaxyproject.org/singularity/svtk:0.0.20190615--py37h73a75cf_2':
|
||
|
|
'quay.io/biocontainers/svtk:0.0.20190615--py37h73a75cf_2' }"
|
||
|
|
|
||
|
|
input:
|
||
|
|
tuple val(meta), path(vcf)
|
||
|
|
path fasta_fai
|
||
|
|
|
||
|
|
output:
|
||
|
|
tuple val(meta), path("*.std.vcf.gz"), emit: standardized_vcf
|
||
|
|
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 arguments = args.args ?: ''
|
||
|
|
def caller = args.caller ?: 'delly'
|
||
|
|
|
||
|
|
def VERSION = '0.0.20190615' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
|
||
|
|
|
||
|
|
def contigs = fasta_fai ? "--contigs ${fasta_fai}" : ""
|
||
|
|
|
||
|
|
"""
|
||
|
|
svtk standardize \\
|
||
|
|
${arguments} \\
|
||
|
|
${contigs} \\
|
||
|
|
${vcf} \\
|
||
|
|
${prefix}.std.vcf.gz \\
|
||
|
|
${caller}
|
||
|
|
|
||
|
|
cat <<-END_VERSIONS > versions.yml
|
||
|
|
"${task.process}":
|
||
|
|
svtk: ${VERSION}
|
||
|
|
END_VERSIONS
|
||
|
|
"""
|
||
|
|
}
|