nf-core_modules/software/rsem/calculateexpression/main.nf
Harshil Patel dce27b8102
Update functions.nf to be more flexible for publishing by meta keys (#423)
* Update functions.nf

* Replace saveAs line in module main script

* Add spacing for ECLint
2021-04-09 17:23:56 +01:00

61 lines
2.4 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process RSEM_CALCULATEEXPRESSION {
tag "$meta.id"
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
} else {
container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
}
input:
tuple val(meta), path(reads)
path index
output:
tuple val(meta), path("*.genes.results") , emit: counts_gene
tuple val(meta), path("*.isoforms.results"), emit: counts_transcript
tuple val(meta), path("*.stat") , emit: stat
tuple val(meta), path("*.log") , emit: logs
path "*.version.txt" , emit: version
tuple val(meta), path("*.STAR.genome.bam") , optional:true, emit: bam_star
tuple val(meta), path("${prefix}.genome.bam") , optional:true, emit: bam_genome
tuple val(meta), path("${prefix}.transcript.bam"), optional:true, emit: bam_transcript
script:
def software = getSoftwareName(task.process)
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def strandedness = ''
if (meta.strandedness == 'forward') {
strandedness = '--strandedness forward'
} else if (meta.strandedness == 'reverse') {
strandedness = '--strandedness reverse'
}
def paired_end = meta.single_end ? "" : "--paired-end"
"""
INDEX=`find -L ./ -name "*.grp" | sed 's/.grp//'`
rsem-calculate-expression \\
--num-threads $task.cpus \\
--temporary-folder ./tmp/ \\
$strandedness \\
$paired_end \\
$options.args \\
$reads \\
\$INDEX \\
$prefix
rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt
"""
}