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cd22a76c78
* correct md5sum for updated star/samtools * merge changes in align test.yml * update md5sum for star genomegenerate * update md5sum for star align
96 lines
3.2 KiB
Text
96 lines
3.2 KiB
Text
process STAR_GENOMEGENERATE {
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tag "$fasta"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.15.1 conda-forge::gawk=5.1.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' :
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'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0' }"
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input:
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path fasta
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path gtf
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output:
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path "star" , emit: index
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def args_list = args.tokenize()
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def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
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if (args_list.contains('--genomeSAindexNbases')) {
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"""
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mkdir star
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STAR \\
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--runMode genomeGenerate \\
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--genomeDir star/ \\
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--genomeFastaFiles $fasta \\
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--sjdbGTFfile $gtf \\
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--runThreadN $task.cpus \\
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$memory \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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star: \$(STAR --version | sed -e "s/STAR_//g")
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
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END_VERSIONS
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"""
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} else {
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"""
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samtools faidx $fasta
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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`
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mkdir star
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STAR \\
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--runMode genomeGenerate \\
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--genomeDir star/ \\
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--genomeFastaFiles $fasta \\
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--sjdbGTFfile $gtf \\
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--runThreadN $task.cpus \\
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--genomeSAindexNbases \$NUM_BASES \\
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$memory \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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star: \$(STAR --version | sed -e "s/STAR_//g")
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
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END_VERSIONS
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"""
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}
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stub:
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"""
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mkdir star
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touch star/Genome
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touch star/Log.out
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touch star/SA
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touch star/SAindex
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touch star/chrLength.txt
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touch star/chrName.txt
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touch star/chrNameLength.txt
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touch star/chrStart.txt
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touch star/exonGeTrInfo.tab
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touch star/exonInfo.tab
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touch star/geneInfo.tab
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touch star/genomeParameters.txt
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touch star/sjdbInfo.txt
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touch star/sjdbList.fromGTF.out.tab
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touch star/sjdbList.out.tab
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touch star/transcriptInfo.tab
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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star: \$(STAR --version | sed -e "s/STAR_//g")
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
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END_VERSIONS
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"""
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}
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