nf-core_modules/modules/bbmap/pileup/main.nf
Edmund Miller 6806cd1de9
feat(bbmap): Initialize pileup module (#1441)
* feat(bbmap): Initialize pileup module

* test(bbmap): Update outputs

* test(bbmap): Add pileup tags

* style(bbmap): Add in when

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-03-24 17:38:24 -06:00

39 lines
1.4 KiB
Text

process BBMAP_PILEUP {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.13 pigz=2.6" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' :
'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' }"
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*.stats.txt"), emit: covstats
tuple val(meta), path("*.hist.txt") , emit: hist
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
pileup.sh \\
-Xmx${task.memory.toGiga()}g \\
in=${bam} \\
out=${prefix}.coverage.stats.txt \\
hist=${prefix}.coverage.hist.txt \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bbmap: \$(bbversion.sh)
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
}