nf-core_modules/modules/rsem/calculateexpression/main.nf
2022-02-04 09:53:32 +01:00

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process RSEM_CALCULATEEXPRESSION {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' :
'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 "versions.yml" , emit: versions
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
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${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 \\
$args \\
$reads \\
\$INDEX \\
$prefix
cat <<-END_VERSIONS > versions.yml
"${task.process}":
rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
star: \$(STAR --version | sed -e "s/STAR_//g")
END_VERSIONS
"""
}