nf-core_modules/modules/gffread/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
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process GFFREAD {
tag "$gff"
label 'process_low'
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publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0"
} else {
container "quay.io/biocontainers/gffread:0.12.1--h8b12597_0"
}
input:
path gff
output:
path "*.gtf" , emit: gtf
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
"""
gffread $gff $options.args -o ${gff.baseName}.gtf
echo \$(gffread --version 2>&1) > ${software}.version.txt
"""
}