mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
34 lines
1.2 KiB
Text
34 lines
1.2 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
def options = initOptions(params.options)
|
|
|
|
process SAMTOOLS_VIEW {
|
|
tag "$meta.id"
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
|
|
|
conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
|
|
} else {
|
|
container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(bam)
|
|
|
|
output:
|
|
tuple val(meta), path("*.bam"), emit: bam
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
"""
|
|
samtools view $options.args $bam > ${prefix}.bam
|
|
echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|