nf-core_modules/modules/samtools/merge/main.nf
2022-07-18 11:37:45 +02:00

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process SAMTOOLS_MERGE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
input:
tuple val(meta), path(input_files, stageAs: "?/*")
path fasta
path fai
output:
tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam
tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def file_type = input_files[0].getExtension()
def reference = fasta ? "--reference ${fasta}" : ""
"""
samtools \\
merge \\
--threads ${task.cpus-1} \\
$args \\
${reference} \\
${prefix}.${file_type} \\
$input_files
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
stub:
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def file_type = input_files[0].getExtension()
"""
touch ${prefix}.${file_type}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}