mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
41 lines
1.1 KiB
Text
41 lines
1.1 KiB
Text
process WHAMG {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::wham=1.8.0" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/wham:1.8.0.1.2017.05.03--h8b12597_1':
|
|
'quay.io/biocontainers/wham:1.8.0.1.2017.05.03--h8b12597_1' }"
|
|
|
|
input:
|
|
tuple val(meta), path(bam), path(bai)
|
|
path(fasta)
|
|
|
|
output:
|
|
tuple val(meta), path("*.vcf.gz"), emit: vcf
|
|
path("*.txt") , emit: graph, optional: true
|
|
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}"
|
|
|
|
"""
|
|
whamg \\
|
|
-x $task.cpus \\
|
|
-f $bam \\
|
|
-a $fasta \\
|
|
$args \\
|
|
> ${prefix}.vcf
|
|
|
|
gzip ${prefix}.vcf
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
whamg: \$(echo \$(whamg 2>&1 | grep Version | sed 's/^Version: v//; s/-.*\$//' ))
|
|
END_VERSIONS
|
|
"""
|
|
}
|