nf-core_modules/modules/rsem/calculateexpression/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
options = initOptions(params.options)
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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']) }
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conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
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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 "versions.yml" , emit: versions
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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:
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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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
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
star: \$(STAR --version | sed -e "s/STAR_//g")
END_VERSIONS
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"""
}