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

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process SAMTOOLS_AMPLICONCLIP {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
input:
tuple val(meta), path(bam)
path bed
val save_cliprejects
val save_clipstats
output:
tuple val(meta), path("*.bam") , emit: bam
tuple val(meta), path("*.clipstats.txt") , optional:true, emit: stats
tuple val(meta), path("*.cliprejects.bam"), optional:true, emit: rejects_bam
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}"
def rejects = save_cliprejects ? "--rejects-file ${prefix}.cliprejects.bam" : ""
def stats = save_clipstats ? "-f ${prefix}.clipstats.txt" : ""
if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
"""
samtools \\
ampliconclip \\
$args \\
$rejects \\
$stats \\
-b $bed \\
-o ${prefix}.bam \\
$bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}