mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-20 23:32:05 +00:00
b5aa12ad3b
* new module: samtools/getrg * add output file to stub * add missing config * Intentionally break prettier linting * [automated] Fix linting with Prettier Co-authored-by: Phil Ewels <phil@seqera.io> Co-authored-by: nf-core-bot <core@nf-co.re>
47 lines
1.3 KiB
Text
47 lines
1.3 KiB
Text
process SAMTOOLS_GETRG {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
|
|
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(input)
|
|
|
|
output:
|
|
tuple val(meta), file("readgroups.txt"), emit: readgroup
|
|
path "versions.yml", emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
"""
|
|
samtools \\
|
|
view \\
|
|
-H \\
|
|
$args \\
|
|
$input \\
|
|
| grep '^@RG' > readgroups.txt
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
|
|
stub:
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
"""
|
|
|
|
echo -e "@RG\\tID:${prefix}\\tSM:${prefix}\\tPL:ILLUMINA" > readgroups.txt
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|