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

40 lines
1.3 KiB
Text
Raw Normal View History

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:'') }
2020-10-12 15:20:35 +00:00
container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
//container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
2020-09-10 15:09:54 +00:00
2020-10-12 15:20:35 +00:00
conda (params.conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
2020-09-10 15:09:54 +00:00
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
"""
}