nf-core_modules/modules/cmseq/polymut/main.nf
2022-06-27 10:35:41 +02:00

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process CMSEQ_POLYMUT {
tag "$meta.id"
label 'process_low'
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
conda (params.enable_conda ? "bioconda::cmseq=1.0.4" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cmseq:1.0.4--pyhb7b1952_0' :
'quay.io/biocontainers/cmseq:1.0.4--pyhb7b1952_0' }"
input:
tuple val(meta), path(bam), path(bai), path(gff), path(fasta)
output:
tuple val(meta), path("*.txt"), emit: polymut
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 fasta_refid = fasta ? "-c $fasta" : ""
def sortindex = bai ? "" : "--sortindex"
def VERSION = '1.0.4' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
polymut.py \\
$args \\
$sortindex \\
$fasta_refid \\
--gff_file $gff \\
$bam > ${prefix}.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cmseq: $VERSION
END_VERSIONS
"""
}