mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
fix: update samtools_merge (#582)
* fix: update samtools_merge * Update modules/samtools/merge/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
parent
65ab646870
commit
adfb8a3d65
2 changed files with 5 additions and 5 deletions
|
@ -22,14 +22,14 @@ process SAMTOOLS_MERGE {
|
|||
tuple val(meta), path(bams)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*merged.bam"), emit: merged_bam
|
||||
tuple val(meta), path("${prefix}.bam"), emit: bam
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
"""
|
||||
samtools merge ${prefix}_merged.bam $bams
|
||||
samtools merge ${prefix}.bam $bams
|
||||
echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
|
||||
"""
|
||||
}
|
||||
|
|
|
@ -2,7 +2,7 @@
|
|||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { SAMTOOLS_MERGE } from '../../../../modules/samtools/merge/main.nf' addParams( options: [:] )
|
||||
include { SAMTOOLS_MERGE } from '../../../../modules/samtools/merge/main.nf' addParams( options: [suffix:'_merged'] )
|
||||
|
||||
workflow test_samtools_merge {
|
||||
input = [ [ id: 'test' ], // meta map
|
||||
|
|
Loading…
Reference in a new issue