nf-core_modules/modules/samtools/depth/main.nf
FriederikeHanssen 1ad73f1b2a
update samtools version to 1.15 (#1358)
* update samtools version to 1.15

* Update checksums
2022-02-28 12:42:29 +01:00

35 lines
976 B
Text

process SAMTOOLS_DEPTH {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
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 \\
$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
"""
}