pipeline/pipeline.wdl

import "./wdl/task.wdl" as mytask
import "./wdl/qc.wdl"
import "./wdl/alignment.wdl"
import "./wdl/call_mutation.wdl"
import "./wdl/fusion.wdl"
import "./wdl/statistics.wdl"
import "./wdl/cnv.wdl"
import "./wdl/msi.wdl"
import "./wdl/chemo.wdl"

workflow pipeline {

    String tumor
    String? normal
    Boolean umi=false

    String input_dir
    String output_dir

    String bed
    String project
    String cancer

    String codes_dir="/home/zhangchao/project/pipeline/workflow/script"
    String ref = "/dataseq/jmdna/database/genome/hg19/hg19.fa"

    String workdir="${output_dir}"

    call mytask.create_dir as create_dir {
        input:
            workdir=workdir
    }

    call qc.qc as qc {
        input:
            tumor=tumor,
            normal=normal,
            umi=umi,
            input_dir=input_dir,
            output_dir=workdir
    }

    call alignment.alignment as alignment {

        input:
            tumor=tumor,
            tumor_r1=qc.tumor_r1,
            tumor_r2=qc.tumor_r2,

            normal=normal,
            normal_r1=qc.normal_r1,
            normal_r2=qc.normal_r2,

            umi=umi,

            ref=ref,
            bed=bed,
            output_dir=workdir
    }

    call statistics.statistics as statistics {
        input:
            tumor=tumor,
            tumor_rmdup_bam=alignment.tumor_rmdup_bam,
            normal=normal,
            normal_rmdup_bam=alignment.normal_rmdup_bam,
            ref=ref,
            bed=bed,
            output_dir=workdir
    }

    call call_mutation.call_mutation as call_mutation {
        input:
            tumor=tumor,
            tumor_rmdup_bam=alignment.tumor_rmdup_bam,
            normal=normal,
            normal_rmdup_bam=alignment.normal_rmdup_bam,

            umi=umi,
            ref=ref,
            bed=bed,
            output_dir=workdir,
            project=project
    }

    call fusion.call_fusion as call_fusion {
        input:
            name=tumor,
            sorted_bam=alignment.tumor_sorted_bam,
            rmdup_bam=alignment.tumor_rmdup_bam,
            output_dir=output_dir,
            ref=ref,
            umi=umi,
            tumor_bamdst_depth=statistics.tumor_bamdst_depth,
            project=project,
            cancer=cancer
    }

    call cnv.call_cnv as call_cnv {
        input:
            tumor=tumor,
            tumor_rmdup_bam=alignment.tumor_rmdup_bam,
            normal=normal,
            normal_rmdup_bam=alignment.normal_rmdup_bam,
            ref=ref,
            bed=bed,
            output_dir=workdir,
            project=project,
            cancer=cancer
    }

    call msi.call_msi as call_msi {
        input:
            tumor=tumor,
            tumor_rmdup_bam=alignment.tumor_rmdup_bam,
            normal=normal,
            normal_rmdup_bam=alignment.normal_rmdup_bam,
            bed=bed,
            output_dir=workdir,
    }

    call chemo.chemo as call_chemo {
        input:
            name=tumor,
            output_dir=workdir,
            project=project,
            vcf=call_mutation.germline_vcf
    }

}