pipeline/pipeline.wdl

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"
import "./wdl/hereditary.wdl"
import "./wdl/pollution.wdl"
import "./wdl/tmb.wdl"
import "./wdl/postprocess.wdl"
import "./wdl/neoantigen.wdl"

workflow pipeline {

    String tumor
    String? normal
    Boolean umi=false

    String input_dir
    String output_dir

    String probe

    String project
    String cancer

    String bed="$WORKFLOW/codes/public/bed/${probe}.bed"
    String ref = "/home/install/ref/hg19/hg19.fa"

    String workdir="${output_dir}"

    Map[String, Boolean] catecode

    call qc.qc as qc {
        input:
            run=catecode['addQc'],
            tumor=tumor,
            normal=normal,
            umi=umi,
            input_dir=input_dir,
            output_dir=workdir
    }

    call alignment.alignment as alignment {

        input:
            run=catecode['addAlignment'],

            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:
            run=catecode['addAlignment'],
            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:
            run=catecode['addTarget'],

            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,
            cancer=cancer,
            probe=probe
    }

    call tmb.call_tmb as call_tmb {
        input:
            run=catecode['addTmb'],
            name=tumor,
            output_dir=workdir,
            project=project,
            umi=umi,
            file=call_mutation.somatic_anno_txt

    }

    call fusion.call_fusion as call_fusion {
        input:
            run=catecode['addFusion'],
            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:
            run=catecode['addCnv'],
            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,
            probe=probe
    }

    call msi.call_msi as call_msi {
        input:
            run=catecode['addMsi'],
            tumor=tumor,
            tumor_rmdup_bam=alignment.tumor_rmdup_bam,
            normal=normal,
            normal_rmdup_bam=alignment.normal_rmdup_bam,
            bed=bed,
            output_dir=workdir
    }

    call hereditary.call_hereditary as call_hereditary {
        input:
            run=catecode['addHcs'],
            name=tumor,
            output_dir=workdir,
            project=project,
            filter_txt=call_mutation.germline_filter
    }

    call chemo.call_chemo as call_chemo {
        input:
            run=catecode['addChemo'],
            name=tumor,
            output_dir=workdir,
            probe=probe,
            vcf=call_mutation.germline_vcf,
            cancer=cancer,
            project=project
    }

    call neoantigen.call_neoantigen as call_neoantigen {
        input:
            run=catecode['addNeoantigen'],
            tumor=tumor,
            normal=normal,
            output_dir=workdir,
            input_dir=input_dir,
            ref=ref,
            tumor_rmdup_bam=alignment.tumor_rmdup_bam,
            somatic_vcf=call_mutation.somatic_vcf,
            germline_vcf=call_mutation.germline_vcf,
            umi=umi
    }

    call pollution.call_pollution as call_pollution {
        input:
            run=catecode['addPollution'],
            tumor=tumor,
            normal=normal,
            output_dir=workdir,
            probe=probe,
            raw_vcf=call_mutation.raw_vcf,
            somatic_vcf=call_mutation.somatic_vcf,
            germline_vcf=call_mutation.germline_vcf
    }

    call postprocess.call_postprocess as call_postprocess {
        input:
            run=catecode['addAutoReport'],
            mutation=call_mutation.somatic_filter,
            fusion=call_fusion.fusion_vcf,
            cnv=call_cnv.cnv_filter,
            msi=call_msi.msi_txt,
            hereditary=call_hereditary.hereditary_txt,
            chemo=call_chemo.chemo_res,
            pollution=call_pollution.pollution_res,
            name=tumor,
            normal=normal,
            output_dir=workdir,
            cancer=cancer,
            project=project
    }

    output {
        String result = "${output_dir}/report/${tumor}.merged_file.xlsx"
    }
}