mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
48 lines
1.5 KiB
Text
48 lines
1.5 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process SEQTK_SUBSEQ {
|
|
tag '$sequences'
|
|
label 'process_low'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
|
|
|
conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3"
|
|
} else {
|
|
container "quay.io/biocontainers/seqtk:1.3--h5bf99c6_3"
|
|
}
|
|
|
|
input:
|
|
path sequences
|
|
path filter_list
|
|
|
|
output:
|
|
path "*.gz" , emit: sequences
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def prefix = options.suffix ?: ''
|
|
def ext = "fa"
|
|
if ("$sequences" ==~ /.+\.fq|.+\.fq.gz|.+\.fastq|.+\.fastq.gz/) {
|
|
ext = "fq"
|
|
}
|
|
"""
|
|
seqtk \\
|
|
subseq \\
|
|
$options.args \\
|
|
$sequences \\
|
|
$filter_list | \\
|
|
gzip --no-name > ${sequences}${prefix}.${ext}.gz
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|