mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 05:13:09 +00:00
33 lines
1,005 B
Text
33 lines
1,005 B
Text
process TABIX_BGZIPTABIX {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? 'bioconda::tabix=1.11' : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' :
|
|
'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(input)
|
|
|
|
output:
|
|
tuple val(meta), path("*.gz"), path("*.tbi"), emit: gz_tbi
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def args2 = task.ext.args2 ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
"""
|
|
bgzip -c $args $input > ${prefix}.gz
|
|
tabix $args2 ${prefix}.gz
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|