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

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process SEQTK_SUBSEQ {
tag '$sequences'
label 'process_low'
conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
container "${ 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:
path sequences
path filter_list
output:
path "*.gz" , emit: sequences
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: ''
def ext = "fa"
if ("$sequences" ==~ /.+\.fq|.+\.fq.gz|.+\.fastq|.+\.fastq.gz/) {
ext = "fq"
}
"""
seqtk \\
subseq \\
$args \\
$sequences \\
$filter_list | \\
gzip --no-name > ${sequences}${prefix}.${ext}.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
}