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

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process SAMTOOLS_COLLATE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
container "${ 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)
path fasta
output:
tuple val(meta), path("*.bam"), emit: bam, optional: true
tuple val(meta), path("*.cram"), emit: cram, optional: true
tuple val(meta), path("*.sam"), emit: sam, optional: true
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 reference = fasta ? "--reference ${fasta}" : ""
def extension = args.contains("--output-fmt sam") ? "sam" :
args.contains("--output-fmt bam") ? "bam" :
args.contains("--output-fmt cram") ? "cram" :
"bam"
if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
"""
samtools \\
collate \\
$args \\
${reference} \\
-@ $task.cpus \\
-o ${prefix}.${extension} \\
$input
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
END_VERSIONS
"""
}