nf-core_modules/modules/samblaster/main.nf
2022-02-04 09:53:32 +01:00

37 lines
1.4 KiB
Text

process SAMBLASTER {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::samblaster=0.1.26 bioconda::samtools=1.14" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:ba4a02b56f3e524a6e006bcd99fe8cc1d7fe09eb-0' :
'quay.io/biocontainers/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:ba4a02b56f3e524a6e006bcd99fe8cc1d7fe09eb-0' }"
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*.bam"), emit: bam
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def args3 = task.ext.args3 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if( "$bam" == "${prefix}.bam" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
"""
samtools view -h $args2 $bam | \\
samblaster $args | \\
samtools view $args3 -Sb - >${prefix}.bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samblaster: \$( samblaster -h 2>&1 | head -n 1 | sed 's/^samblaster: Version //' )
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}