CNVkit_Sequenza/tasks/CNVkit.wdl

task cnvkit{
    String sample_id
    File ref_dir
    String? fasta
    File ref_flat
    #File hrd
    File tumor_bam
    File tumor_bam_index
    File? normal_bam
    File? normal_bam_index
    String docker
    String cluster_config
    String disk_size
    String sample=basename(tumor_bam,".bam")

    command <<<

        set -o pipefail
        set -e
        nt=$(nproc)
        
        echo ${sample}

        /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} -n ${normal_bam} -m wgs -f ${ref_dir} --annotate ${ref_flat} -p $nt

                  
        # Check noise
    	/root/miniconda2/bin/cnvkit.py metrics ${sample}.cnr -s ${sample}.cns > ${sample}.stats
    
        # Derive each segment's absolute integer copy number, ploidy must be int value
        #PURITY=`awk -F'\t' '{print $6}' ${hrd} | sed -n '2p'`
        PURITY=3.3
        /root/miniconda2/bin/cnvkit.py segmetrics ${sample}.cnr -s ${sample}.cns --ci -o ${sample}.segmetrics.cns
        /root/miniconda2/bin/cnvkit.py call ${sample}.segmetrics.cns --drop-low-coverage --filter ci -m threshold --purity $PURITY -o ${sample}.call.cns
          

        /root/miniconda2/bin/cnvkit.py genemetrics ${sample}.cnr -t 0.2 -m 3 -o ${sample}.ratio_cnv.txt

        /root/miniconda2/bin/cnvkit.py genemetrics ${sample}.cnr -s ${sample}.call.cns -t 0.2 -m 3 -o ${sample}.segment_cnv.txt


        /root/miniconda2/bin/cnvkit.py scatter ${sample}.cnr -s ${sample}.call.cns -o ${sample}_scatter.pdf

        /root/miniconda2/bin/cnvkit.py diagram ${sample}.cnr -s ${sample}.call.cns -o ${sample}.diagram.pdf

        /root/miniconda2/bin/cnvkit.py heatmap ${sample}.cnr ${sample}.call.cns -o ${sample}.heatmap.pdf

        cat ${sample}.ratio_cnv.txt | tail -n+2 | cut -f1 | sort | uniq > ratio_cnv.txt
        cat ${sample}.segment_cnv.txt | tail -n+2 | cut -f1 | sort | uniq > segment_cnv.txt
        comm -12 ratio_cnv.txt segment_cnv.txt > ${sample}.trusted_genes.txt

        awk 'NR==FNR {a[$1]=$2;next} NR!=FNR {if(FNR == 1 || (FNR != 1 && $1 in a)) print $0}' ${sample}.trusted_genes.txt ${sample}.ratio_cnv.txt > ${sample}.ratio_cnv.trusted.txt
        /root/miniconda2/bin/cnvkit.py call ${sample}.ratio_cnv.trusted.txt -m threshold -o ${sample}.ratio_cnv.call.txt
        awk '{if ($6 != 2) print $0}' ${sample}.ratio_cnv.call.txt > ${sample}.ratio_cnv.call.filter.txt
        
        cp ${sample}.ratio_cnv.call.filter.txt ${sample}.ratio_cnv.call.filter.bed

        ls ./

        tar cvf ${sample}.tar ${sample}*

    >>>

    runtime{
        docker:docker
        cluster:cluster_config
        systemDisk:"cloud_ssd 40"
        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
        timeout:259200
    }

    output{
        File out_file = "${sample}.tar"
        File cnv_bed = "${sample}.ratio_cnv.call.filter.bed"
    }

}