nf-core_modules/software/gffread/main.nf
2020-09-10 16:09:54 +01:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
process GFFREAD {
tag "$gff"
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
container "quay.io/biocontainers/gffread:0.11.7--h8b12597_0"
//container https://depot.galaxyproject.org/singularity/gffread:0.11.7--h8b12597_0
conda (params.conda ? "bioconda::gffread=0.11.7" : null)
input:
path gff
val options
output:
path "*.gtf" , emit: gtf
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
def ioptions = initOptions(options)
"""
gffread $gff $ioptions.args -o ${gff.baseName}.gtf
echo \$(gffread --version 2>&1) > ${software}.version.txt
"""
}