mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
38 lines
1.3 KiB
Text
38 lines
1.3 KiB
Text
|
// Import generic module functions
|
||
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||
|
|
|
||
|
|
params.options = [:]
|
||
|
|
options = initOptions(params.options)
|
||
|
|
|
||
|
|
process TABIX_BGZIPTABIX {
|
||
|
|
tag "$meta.id"
|
||
|
|
label 'process_medium'
|
||
|
|
publishDir "${params.outdir}",
|
||
|
|
mode: params.publish_dir_mode,
|
||
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||
|
|
|
||
|
|
conda (params.enable_conda ? "bioconda::tabix=0.2.6" : null)
|
||
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||
|
|
container "https://depot.galaxyproject.org/singularity/tabix:0.2.6--ha92aebf_0"
|
||
|
|
} else {
|
||
|
|
container "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
|
||
|
|
}
|
||
|
|
|
||
|
|
input:
|
||
|
|
tuple val(meta), path(input)
|
||
|
|
|
||
|
|
output:
|
||
|
|
tuple val(meta), path("*.gz"), path("*.tbi"), emit: tbi
|
||
|
|
path "*.version.txt", emit: version
|
||
|
|
|
||
|
|
script:
|
||
|
|
def software = getSoftwareName(task.process)
|
||
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||
|
|
"""
|
||
|
|
bgzip -c $options.args $input > ${prefix}.gz
|
||
|
|
tabix $options.args2 ${prefix}.gz
|
||
|
|
|
||
|
|
echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/(.*\$//' > ${software}.version.txt
|
||
|
|
"""
|
||
|
|
}
|