task batch {
    String sample_id
    Array[File] tumor_bam
    Array[File] tumor_bai
    Array[File] normal_bam
    Array[File] normal_bai
    File bed
    File faidx
    File fasta
    File? ref_flat
    File access_bed
    File? reference
    String method
    String segment_method
    String docker
    String cluster_config
    String disk_size

    String annotate_opt = if (ref_flat != "") then "--annotate ref_flat.txt" else ""
    String reference_opt = if (reference != "") then "--reference my_reference.cnn" else ""
    String access_opt = if (method == "amplicon") then "--access amplicon.bed" else "--access access-mappable.bed"

    command <<<
        set -o pipefail
        set -e
        mkdir -p /cromwell_root/tmp/cnvkit
        cp ${sep=' ' normal_bai} /cromwell_root/tmp/cnvkit
        cp ${sep=' ' tumor_bai} /cromwell_root/tmp/cnvkit
        # must exist parameters
        cp ${fasta} /cromwell_root/tmp/cnvkit/hg38.fa
        cp ${faidx} /cromwell_root/tmp/cnvkit/hg38.fai
        cp ${access_bed} /cromwell_root/tmp/cnvkit/access-mappable.bed
        # optional parameters
        if [ ${method} == "amplicon" ]; then cp ${bed} /cromwell_root/tmp/cnvkit/amplicon.bed; fi
        if [ ${ref_flat} != "" ]; then cp ${ref_flat} /cromwell_root/tmp/cnvkit/ref_flat.txt; fi
        if [ ${reference} != "" ]; then cp ${reference} /cromwell_root/tmp/cnvkit/my_reference.cnn; fi
        cd /cromwell_root/tmp/cnvkit
        
        mkdir results
        cnvkit.py batch ${sep=' ' tumor_bam} --normal ${sep=' ' normal_bam} \
        --method ${method} --segment-method ${segment_method} \
        --targets ${bed} ${access_opt} ${annotate_opt} \
        --fasta hg38.fa ${reference_opt} \
        --output-reference ${sample_id}.reference.cnn \
        --output-dir ./results/ \
        --drop-low-coverage --diagram --scatter
    >>>

    runtime { 
        docker: docker
        cluster: cluster_config
        systemDisk: "cloud_ssd 40"
        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
    }

    output {
        File reference_cnn = "${sample_id}.reference.cnn"
        Array[File] results = glob("/cromwell_root/tmp/cnvkit/results/*")
    }
}