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 """ }