nf-core_modules/software/gffread/main.nf

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