mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
32 lines
1.2 KiB
Text
32 lines
1.2 KiB
Text
process SAMTOOLS_MERGE {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
|
|
'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(input_files)
|
|
path fasta
|
|
|
|
output:
|
|
tuple val(meta), path("${prefix}.bam"), optional:true, emit: bam
|
|
tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
prefix = task.ext.prefix ?: "${meta.id}"
|
|
def file_type = input_files[0].getExtension()
|
|
def reference = fasta ? "--reference ${fasta}" : ""
|
|
"""
|
|
samtools merge --threads ${task.cpus-1} $args ${reference} ${prefix}.${file_type} $input_files
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|