mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
39 lines
1.2 KiB
Text
39 lines
1.2 KiB
Text
process GSTAMA_MERGE {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::gs-tama=1.0.2" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/gs-tama:1.0.2--hdfd78af_0' :
|
|
'quay.io/biocontainers/gs-tama:1.0.2--hdfd78af_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(bed)
|
|
path filelist
|
|
|
|
output:
|
|
tuple val(meta), path("*.bed") , emit: bed
|
|
tuple val(meta), path("*_gene_report.txt") , emit: gene_report
|
|
tuple val(meta), path("*_merge.txt") , emit: merge
|
|
tuple val(meta), path("*_trans_report.txt"), emit: trans_report
|
|
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}"
|
|
"""
|
|
tama_merge.py \\
|
|
-f $filelist \\
|
|
-d merge_dup \\
|
|
-p ${prefix} \\
|
|
$args
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
gstama: \$( tama_merge.py -version | head -n1 )
|
|
END_VERSIONS
|
|
"""
|
|
}
|