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

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process SEQTK_SAMPLE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' :
'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }"
input:
tuple val(meta), path(reads)
val sample_size
output:
tuple val(meta), path("*.fastq.gz"), emit: reads
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}"
if (meta.single_end) {
"""
seqtk \\
sample \\
$args \\
$reads \\
$sample_size \\
| gzip --no-name > ${prefix}.fastq.gz \\
cat <<-END_VERSIONS > versions.yml
"${task.process}":
seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
} else {
if (!(args ==~ /.*-s[0-9]+.*/)) {
args += " -s100"
}
"""
seqtk \\
sample \\
$args \\
${reads[0]} \\
$sample_size \\
| gzip --no-name > ${prefix}_1.fastq.gz \\
seqtk \\
sample \\
$args \\
${reads[1]} \\
$sample_size \\
| gzip --no-name > ${prefix}_2.fastq.gz \\
cat <<-END_VERSIONS > versions.yml
"${task.process}":
seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
}
}