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

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process SAMTOOLS_FASTQ {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
container "${ 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)
output:
tuple val(meta), path("*.fastq.gz"), emit: fastq
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 endedness = meta.single_end ? "-0 ${prefix}.fastq.gz" : "-1 ${prefix}_1.fastq.gz -2 ${prefix}_2.fastq.gz"
"""
samtools \\
fastq \\
$args \\
--threads ${task.cpus-1} \\
$endedness \\
$bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}