nf-core_modules/modules/samtools/depth/main.nf
Matthieu Muffato f0a86eaf5b
Multithreaded samtools commands (#2080)
* Multithreaded samtools commands

* Updated the checksums since the BAM files include the actual command line

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
2022-09-26 17:44:36 +01:00

36 lines
1,018 B
Text

process SAMTOOLS_DEPTH {
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(bam)
output:
tuple val(meta), path("*.tsv"), emit: tsv
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 \\
depth \\
--threads ${task.cpus-1} \\
$args \\
-o ${prefix}.tsv \\
$bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}