nf-core_modules/modules/cnvkit/batch/main.nf

process CNVKIT_BATCH {
    tag "$meta.id"
    label 'process_low'

    conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9 bioconda::samtools=1.15.1' : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0' :
        'quay.io/biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0' }"

    input:
    tuple val(meta), path(tumor), path(normal)
    path  fasta
    path  fasta_fai
    path  targets
    path  reference

    output:
    tuple val(meta), path("*.bed"), emit: bed
    tuple val(meta), path("*.cnn"), emit: cnn, optional: true
    tuple val(meta), path("*.cnr"), emit: cnr, optional: true
    tuple val(meta), path("*.cns"), emit: cns, optional: true
    tuple val(meta), path("*.pdf"), emit: pdf, optional: true
    tuple val(meta), path("*.png"), emit: png, optional: true
    path "versions.yml"           , emit: versions

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

    script:
    def args = task.ext.args ?: ''

    def tumor_exists = tumor ? true : false
    def normal_exists = normal ? true : false

    // execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow
    def tumor_cram = tumor_exists && tumor.Extension == "cram" ? true : false
    def normal_cram = normal_exists && normal.Extension == "cram" ? true : false
    def tumor_bam = tumor_exists && tumor.Extension == "bam" ? true : false
    def normal_bam = normal_exists && normal.Extension == "bam" ? true : false

    def tumor_out = tumor_cram ? tumor.BaseName + ".bam" : "${tumor}"

    // tumor_only mode does not need fasta & target
    // instead it requires a pre-computed reference.cnn which is built from fasta & target
    def (normal_out, normal_args, fasta_args) = ["", "", ""]
    def fai_reference = fasta_fai ? "--fai-reference ${fasta_fai}" : ""

    if (normal_exists){
        def normal_prefix = normal.BaseName
        normal_out = normal_cram ? "${normal_prefix}" + ".bam" : "${normal}"
        fasta_args = fasta ? "--fasta $fasta" : ""

        // germline mode
        // normal samples must be input without a flag
        // requires flag --normal to be empty []
        if(!tumor_exists){
            tumor_out = "${normal_prefix}" + ".bam"
            normal_args = "--normal "
        }
        // somatic mode
        else {
            normal_args = normal_prefix ? "--normal $normal_out" : ""
        }
    }

    def target_args = targets ? "--targets $targets" : ""
    def reference_args = reference ? "--reference $reference" : ""

    // somatic_mode cram_input
    if (tumor_cram && normal_cram){
        """
        samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out
        samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $normal_out

        cnvkit.py \\
            batch \\
            $tumor_out \\
            $normal_args \\
            $fasta_args \\
            $reference_args \\
            $target_args \\
            --processes $task.cpus \\
            $args

        cat <<-END_VERSIONS > versions.yml
        "${task.process}":
            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
        END_VERSIONS
        """
    }
    // somatic_mode bam_input
    else if (tumor_bam && normal_bam){
        """
        cnvkit.py \\
            batch \\
            $tumor_out \\
            $normal_args \\
            $fasta_args \\
            $reference_args \\
            $target_args \\
            --processes $task.cpus \\
            $args

        cat <<-END_VERSIONS > versions.yml
        "${task.process}":
            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
        END_VERSIONS
        """
    }
    // tumor_only_mode cram_input
    else if(tumor_cram && !normal_exists){
        """
        samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out

        cnvkit.py \\
            batch \\
            $tumor_out \\
            $normal_args \\
            $fasta_args \\
            $reference_args \\
            $target_args \\
            --processes $task.cpus \\
            $args

        cat <<-END_VERSIONS > versions.yml
        "${task.process}":
            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
        END_VERSIONS
        """
    }
    // tumor_only bam_input
    else if(tumor_bam && !normal_exists){
        """
        cnvkit.py \\
            batch \\
            $tumor_out \\
            $normal_args \\
            $fasta_args \\
            $reference_args \\
            $target_args \\
            --processes $task.cpus \\
            $args

        cat <<-END_VERSIONS > versions.yml
        "${task.process}":
            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
        END_VERSIONS
        """
    }
    // germline mode cram_input
    // normal_args must be --normal []
    else if (normal_cram && !tumor_exists){
        """
        samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $tumor_out

        cnvkit.py \\
            batch \\
            $tumor_out \\
            $normal_args \\
            $fasta_args \\
            $reference_args \\
            $target_args \\
            --processes $task.cpus \\
            $args

        cat <<-END_VERSIONS > versions.yml
        "${task.process}":
            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
        END_VERSIONS
        """
    }
    // germline mode bam_input
    else if (normal_bam && !tumor_exists){
        """
        cnvkit.py \\
            batch \\
            $tumor_out \\
            $normal_args \\
            $fasta_args \\
            $reference_args \\
            $target_args \\
            --processes $task.cpus \\
            $args

        cat <<-END_VERSIONS > versions.yml
        "${task.process}":
            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
        END_VERSIONS
        """
    }

}