Verified Commit 3dd05762 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

gffread: add main.nf

parent 9eb61947
version = "0.12.2"
container_url = "lbmc/gffread:${version}"
params.gffread = ""
params.gffread_out = ""
process gffread {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_prefix"
if (params.gffread_out != "") {
publishDir "results/${params.gffread_out}", mode: 'copy'
}
input:
tuple val(file_id), path(gtf)
tuple val(fasta_id), path(fasta)
output:
tuple val(fasta_id), path("${file_prefix}.fasta"), emit: fasta
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gffread ${gtf} -g ${fasta} -o ${file_prefix}.fasta
"""
}
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