process STAR_GENOMEGENERATE { tag "$fasta" label 'process_high' conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' : 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' }" input: path fasta path gtf output: path "star" , emit: index path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def args_list = args.tokenize() def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : '' if (args_list.contains('--genomeSAindexNbases')) { """ mkdir star STAR \\ --runMode genomeGenerate \\ --genomeDir star/ \\ --genomeFastaFiles $fasta \\ --sjdbGTFfile $gtf \\ --runThreadN $task.cpus \\ $memory \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": star: \$(STAR --version | sed -e "s/STAR_//g") samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//') END_VERSIONS """ } else { """ samtools faidx $fasta NUM_BASES=`gawk '{sum = sum + \$2}END{if ((log(sum)/log(2))/2 - 1 > 14) {printf "%.0f", 14} else {printf "%.0f", (log(sum)/log(2))/2 - 1}}' ${fasta}.fai` mkdir star STAR \\ --runMode genomeGenerate \\ --genomeDir star/ \\ --genomeFastaFiles $fasta \\ --sjdbGTFfile $gtf \\ --runThreadN $task.cpus \\ --genomeSAindexNbases \$NUM_BASES \\ $memory \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": star: \$(STAR --version | sed -e "s/STAR_//g") samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//') END_VERSIONS """ } stub: """ mkdir star touch star/Genome touch star/Log.out touch star/SA touch star/SAindex touch star/chrLength.txt touch star/chrName.txt touch star/chrNameLength.txt touch star/chrStart.txt touch star/exonGeTrInfo.tab touch star/exonInfo.tab touch star/geneInfo.tab touch star/genomeParameters.txt touch star/sjdbInfo.txt touch star/sjdbList.fromGTF.out.tab touch star/sjdbList.out.tab touch star/transcriptInfo.tab cat <<-END_VERSIONS > versions.yml "${task.process}": star: \$(STAR --version | sed -e "s/STAR_//g") samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//') END_VERSIONS """ }