nf-core_modules/software/rsem/preparereference/main.nf

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2020-09-10 15:09:54 +00:00
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
process RSEM_PREPAREREFERENCE {
tag "$fasta"
label 'process_high'
publishDir "${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/rsem:1.3.3--pl526ha52163a_0"
//container "https://depot.galaxyproject.org/singularity/rsem:1.3.3--pl526ha52163a_0"
conda (params.conda ? "bioconda::rsem=1.3.3" : null)
input:
path fasta
path gtf
val options
output:
path "rsem" , emit: index
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
def ioptions = initOptions(options)
"""
mkdir rsem
rsem-prepare-reference \\
--gtf $gtf \\
--num-threads $task.cpus \\
$ioptions.args \\
$fasta \\
rsem/genome
rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt
"""
}