nf-core_modules/modules/bwamem2/mem/main.nf

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'

params.options = [:]
options        = initOptions(params.options)

process BWAMEM2_MEM {
    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']) }

    conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.12" : null)
    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container "https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:cf603b12db30ec91daa04ba45a8ee0f35bbcd1e2-0"
    } else {
        container "quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:cf603b12db30ec91daa04ba45a8ee0f35bbcd1e2-0"
    }

    input:
    tuple val(meta), path(reads)
    path  index

    output:
    tuple val(meta), path("*.bam"), emit: bam
    path  "versions.yml"          , emit: version

    script:
    def software   = getSoftwareName(task.process)
    def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
    def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
    """
    INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`

    bwa-mem2 \\
        mem \\
        $options.args \\
        $read_group \\
        -t $task.cpus \\
        \$INDEX \\
        $reads \\
        | samtools view $options.args2 -@ $task.cpus -bhS -o ${prefix}.bam -

    cat <<-END_VERSIONS > versions.yml
    ${getProcessName(task.process)}:
        ${getSoftwareName(task.process)}: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
    END_VERSIONS
    """
}