nf-core_modules/modules/seqtk/subseq/main.nf
Harshil Patel e937c7950a
Rename software/ directory to modules/ to re-organise module structure (#567)
* Update README

* Rename pytest_software.yml to pytest_modules.yml

* Rename main software directory to modules

* Remove deprecated modules

* Rename tests software to modules

* Replace paths for tests in pytest_modules.yml

* Replace software with modules in Github Actions

* Replace software with modules in main.nf tests

* Rename software to modules in test.yml
2021-07-07 10:10:18 +01:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } 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 "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
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
echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//' > ${software}.version.txt
"""
}