nf-core_modules/modules/seqtk/seq/main.nf
Thomas A. Christensen II b82d7abe70
Decrease indent in seqtk/seq versions.yml output (#1384)
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-03-09 11:56:35 -05:00

40 lines
1.1 KiB
Text

process SEQTK_SEQ {
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(fastx)
output:
tuple val(meta), path("*.gz") , emit: fastx
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def extension = "fastq"
if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/ || "$args" ==~ /\-[aA]/ ) {
extension = "fasta"
}
"""
seqtk \\
seq \\
$args \\
$fastx | \\
gzip -c > ${prefix}.seqtk-seq.${extension}.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
}