pipeline/pipeline.wdl

import "./wdl/task.wdl" as mytask
import "./wdl/qc.wdl"
import "./wdl/alignment.wdl"
import "./wdl/statistics.wdl"

workflow pipeline {

    String tumor
    String? normal
    String inputDir
    String outputDir
    String cancer
    String project="650gene"
    String codesDir="/dataseq/jmdna/codes/pancancer_controlsample"
    String ref = "/dataseq/jmdna/database/genome/hg19/hg19.fa"
    String bed = "/dataseq/jmdna/database/bed/650.bed"

    String workdir="${outputDir}/${tumor}"

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

    call qc.qc as qc {
        input:
            tumor=tumor,
            normal=normal,
            inputDir=inputDir,
            outputDir=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,

            ref=ref,
            bed=bed,
            outputDir=workdir
    }

    call statistics.statistics as statistics {
        input:
            tumor=tumor,
            tumor_rmdupBam=alignment.tumor_rmdupBam,

            normal=normal,
            normal_rmdupBam=alignment.normal_rmdupBam,

            ref=ref,
            bed=bed,
            outputDir=workdir,
            codesDir=codesDir
    }

    call mytask.conpair as conpair {
        input:
            codesDir=codesDir,
            name=tumor,
            tumor_rmdupBam=alignment.tumor_rmdupBam,
            normal_rmdupBam=alignment.normal_rmdupBam,
            outputDir=workdir,
            ref=ref
    }

    call mytask.mutation_calling as mutation_calling {
        input:
            name=tumor,
            tumor_pileup=alignment.tumor_pileup,
            normal_pileup=alignment.normal_pileup,
            outputDir=workdir
    }

    call mytask.annovar as annovar {
        input:
            name=tumor,
            outputDir=workdir,
            ref=ref,
            somatic_hc_vcf=mutation_calling.somatic_hc_vcf,
            germline_vcf=mutation_calling.germline_vcf,
            loh_hc_vcf=mutation_calling.loh_hc_vcf,
            rmdupBam=alignment.tumor_rmdupBam
    }

    call mytask.dealwithsnvindel as dealwithsnvindel {
        input:
            codesDir=codesDir,
            name=tumor,
            somatic_all_anno=annovar.somatic_all_anno,
            germline_anno=annovar.germline_anno,
            project=project,
            outputDir=workdir,
            cancer=cancer
    }

    call mytask.hereditary as hereditary {
        input:
            codesDir=codesDir,
            name=tumor,
            outputDir=workdir,
            project=project,
            germline_filtered = dealwithsnvindel.germline_filtered
    }

    call mytask.tmb as tmb {
        input:
            codesDir=codesDir,
            name=tumor,
            outputDir=workdir,
            somatic_anno=annovar.somatic_anno
    }

    call mytask.fusion as fusion {
        input:
            name=tumor,
            ref=ref,
            codesDir=codesDir,
            outputDir=workdir,
            rmdupBam=alignment.tumor_rmdupBam,
            cancer=cancer,
            project=project,
            tumor_bamdst_depth=statistics.tumor_bamdst_depth
    }

    call mytask.cnvkit as cnvkit {
        input:
            tumor=tumor,
            normal=normal,

            tumor_rmdupBam=alignment.tumor_rmdupBam,
            normal_rmdupBam=alignment.normal_rmdupBam,
            ref=ref,
            bed=bed,
            outputDir=workdir,
            cancer=cancer,
            codesDir=codesDir,
            project=project,
    }

    call mytask.chemo as chemo {
        input:
            codesDir=codesDir,
            outputDir=workdir,
            normal=normal,
            project=project,
            rmdupBam=alignment.tumor_rmdupBam,
    }

    call mytask.msi as msi {
        input:
            bed=bed,
            name=tumor,
            outputDir=workdir,
            tumor_rmdupBam = alignment.tumor_rmdupBam,
            normal_rmdupBam =alignment.normal_rmdupBam
    }

    call mytask.hla as hla {
        input:
            inputDir=inputDir,
            outputDir=workdir,
            normal=normal,
    }

    call mytask.neoantigen as neoantigen {
        input:
            codesDir=codesDir,
            outputDir=workdir,
            name=tumor,
            somatic_hc_vcf=mutation_calling.somatic_hc_vcf,
            normal=normal,
            hla=hla.hla
    }

    call mytask.mmr as mmr {
        input:
            codesDir=codesDir,
            name=tumor,
            outputDir=workdir,
            germline_filtered = dealwithsnvindel.germline_filtered
    }

    call mytask.hrr as hrr {
        input:
            codesDir=codesDir,
            name=tumor,
            outputDir=workdir,
            germline_filtered = dealwithsnvindel.germline_filtered
    }

    call mytask.hotspot as hotspot {
        input:
            name=tumor,
            outputDir=workdir,
            ref=ref,
            rmdupBam=alignment.tumor_rmdupBam,
            codesDir=codesDir,
    }

    call mytask.auto_report {
        input:
            tumor=tumor,
            normal=normal,
            outputDir=workdir,
            codesDir=codesDir,
            cancer=cancer,
            cnv_cns=cnvkit.cns,
            cnv_png=cnvkit.png,
            fusion_pos=fusion.fusion,
            snvindel_filtered=dealwithsnvindel.snvindel_filtered,
            tmb=tmb.tmb,
            mmr=mmr.mmr,
            hrr=hrr.hrr,
            hereditary_pre=hereditary.hereditary_pre
    }
}