nf-core_modules/modules/samtools/ampliconclip/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process SAMTOOLS_AMPLICONCLIP {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::samtools=1.13" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
} else {
container "quay.io/biocontainers/samtools:1.13--h8c37831_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
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def rejects = save_cliprejects ? "--rejects-file ${prefix}.cliprejects.bam" : ""
def stats = save_clipstats ? "-f ${prefix}.clipstats.txt" : ""
"""
samtools \\
ampliconclip \\
$options.args \\
-@ $task.cpus \\
$rejects \\
$stats \\
-b $bed \\
-o ${prefix}.bam \\
$bam
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}