nf-core_modules/modules/fastk/merge/main.nf

process FASTK_MERGE {
    tag "$meta.id"
    label 'process_medium'

    if (params.enable_conda) {
        error "Conda environments cannot be used when using the FastK tool. Please use docker or singularity containers."
    }
    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
    container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.0'

    input:
    tuple val(meta), path(hist), path(ktab), path(prof)

    output:
    tuple val(meta), path("*.hist")                      , emit: hist
    tuple val(meta), path("*.ktab*", hidden: true)       , emit: ktab, optional: true
    tuple val(meta), path("*.{prof,pidx}*", hidden: true), emit: prof, optional: true
    path "versions.yml"                                  , emit: versions

    when:
    task.ext.when == null || task.ext.when

    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
    def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
    """
    Fastmerge \\
        $args \\
        -T$task.cpus \\
        ${prefix} \\
        $hist

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        fastk: $FASTK_VERSION
    END_VERSIONS
    """
}