nf-core_modules/modules/gatk4/estimatelibrarycomplexity/main.nf

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

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

process GATK4_ESTIMATELIBRARYCOMPLEXITY {
    tag "$meta.id"
    label 'process_medium'
    publishDir "${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::gatk4=4.2.2.0" : null)
    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.2.0--hdfd78af_1"
    } else {
        container "quay.io/biocontainers/gatk4:4.2.2.0--hdfd78af_1"
    }

    input:
    tuple val(meta), path(cram)
    path(fasta)
    path(fai)
    path(dict)

    output:
    tuple val(meta), path('*.metrics'), emit: metrics
    path "versions.yml"                  , emit: versions

    script:
    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
    def crams = cram.collect(){ x -> "-I ".concat(x.toString()) }.join(" ")

    def avail_mem = 3
    if (!task.memory) {
        log.info '[GATK EstimateLibraryComplexity] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
    } else {
        avail_mem = task.memory.giga
    }
    """
    gatk EstimateLibraryComplexity \
        ${crams} \
        -O ${prefix}.metrics \
        --REFERENCE_SEQUENCE ${fasta} \
        --VALIDATION_STRINGENCY SILENT \
        --TMP_DIR . $options.args

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