nf-core_modules/modules/star/genomegenerate/main.nf

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
    """
}