somatic_SNVs_pipeline/workflow_VIP.wdl

import "./tasks/BQSR.wdl" as Sentieon_BQSR
import "./tasks/TNseq.wdl" as TNseq
import "./tasks/TNscope.wdl" as TNscope
import "./tasks/manta.wdl" as manta_calling
import "./tasks/strelka.wdl" as strelka_calling
import "./tasks/bcftools.wdl" as bcftools
import "./tasks/bcftools_concat.wdl" as bcftools_concat
import "./tasks/annovar.wdl" as annovar
import "./tasks/Haplotyper.wdl" as Haplotyper
import "./tasks/MSIsensor.wdl" as MSIsensor
import "./tasks/tmb.wdl" as tmb

#VIP客户（只用TNseq进行call）
workflow {{ project_name }} {
	#sample info
  File? normal_deduped_bam
  File? normal_deduped_bam_bai
	File? tumor_deduped_bam
	File? tumor_deduped_bam_bai
  String sample_id
	String Seq_platform
	#reference fasta
	String ref_fasta
	File ref_fasta_dir
	File annot_gff
  File dbsnp_dir
  File dbmills_dir
  String dbsnp
  String db_mills
	File germline_resource
	File germline_resource_tbi
	File annovar_database
  File? regions
  File baseline
  File hg38_CDS



	#docker
  String docker_fastp
	String docker_sentieon
	String SENTIEON_LICENSE
	String docker_qualimap
	String docker_manta
	String docker_strelka
	String docker_bcftools
	String docker_annovar
  String docker_tmb
  String docker_MSIsensor

	#config
  String cluster_config
  String disk_size
	Boolean? fastqc
	Boolean bamqc
	Boolean Annovar
  Boolean AF_filter


if (normal_deduped_bam != ""){

		call Sentieon_BQSR.Sentieon_BQSR as Sentieon_BQSR_normal{
			input:
				ref_dir=ref_fasta_dir,
				dbsnp_dir=dbsnp_dir,
				dbmills_dir = dbmills_dir,
				sample_id=sample_id+'_N',
				ref_fasta=ref_fasta,
				dbsnp=dbsnp,
				db_mills=db_mills,
				deduped_bam=normal_deduped_bam,
				deduped_bam_index=normal_deduped_bam_bai,
				docker=docker_sentieon,
				cluster_config=cluster_config,
				disk_size=disk_size,
				SENTIEON_LICENSE=SENTIEON_LICENSE
		}

	}

if (tumor_deduped_bam != ""){

		call Sentieon_BQSR.Sentieon_BQSR as Sentieon_BQSR_tumor{
			input:
				ref_dir=ref_fasta_dir,
				dbsnp_dir=dbsnp_dir,
				dbmills_dir = dbmills_dir,
				sample_id=sample_id+'_T',
				ref_fasta=ref_fasta,
				dbsnp=dbsnp,
				db_mills=db_mills,
				deduped_bam=tumor_deduped_bam,
				deduped_bam_index=tumor_deduped_bam_bai,
				docker=docker_sentieon,
				cluster_config=cluster_config,
				disk_size=disk_size,
				SENTIEON_LICENSE=SENTIEON_LICENSE
		}

	}

call MSIsensor.MSIsensor as MSIsensor {
    input:
    sample=sample_id,
    fasta=ref_fasta,
    ref_dir=ref_fasta_dir,
    normal_bam=Sentieon_BQSR_normal.recaled_bam,
    normal_bam_index=Sentieon_BQSR_normal.recaled_bam_index,
    tumor_bam=Sentieon_BQSR_tumor.recaled_bam,
    tumor_bam_index=Sentieon_BQSR_tumor.recaled_bam_index,
    baseline=baseline,
    docker=docker_MSIsensor,
    cluster_config="OnDemand bcs.ps.g.large img-ubuntu-vpc",
    disk_size=disk_size
  }


call Haplotyper.Haplotyper as Haplotyper {
      input:
        SENTIEON_LICENSE=SENTIEON_LICENSE,
        sample=sample_id + '.N',
        fasta=ref_fasta,
        ref_dir=ref_fasta_dir,
        recaled_bam=Sentieon_BQSR_normal.recaled_bam,
        recaled_bam_index=Sentieon_BQSR_normal.recaled_bam_index,
        dbsnp=dbsnp,
        dbsnp_dir=dbsnp_dir,
        regions=regions,
        docker=docker_sentieon,
        disk_size=disk_size,
        cluster_config=cluster_config
    }

call bcftools.bcftools as Haplotyper_bcftools {
      input:
        vcf=Haplotyper.vcf,
        fasta=ref_fasta,
        ref_dir=ref_fasta_dir,
        docker=docker_bcftools,
        cluster_config="OnDemand bcs.ps.g.large img-ubuntu-vpc",
        disk_size=disk_size
    }

call TNseq.sentieon_TNseq as sentieon_TNseq{
	input:
		sample_id = sample_id,
		tumor_bam = Sentieon_BQSR_tumor.recaled_bam,
		tumor_bam_bai = Sentieon_BQSR_tumor.recaled_bam_index,
		normal_bam = Sentieon_BQSR_normal.recaled_bam,
		normal_bam_bai = Sentieon_BQSR_normal.recaled_bam_index,
		tumor_name = sample_id+'_T',
		normal_name = sample_id+'_N',

		ref_dir = ref_fasta_dir,
		ref_fasta = ref_fasta,
		germline_resource = germline_resource,
		germline_resource_tbi = germline_resource_tbi,

		docker = docker_sentieon,
		cluster_config = cluster_config,
		disk_size = disk_size,
		SENTIEON_LICENSE = SENTIEON_LICENSE
}



call bcftools.bcftools as TNseq_bcftools {
	input:
	vcf=sentieon_TNseq.vcf,
	fasta=ref_fasta,
	ref_dir=ref_fasta_dir,
	docker=docker_bcftools,
	cluster_config="OnDemand bcs.ps.g.large img-ubuntu-vpc",
	disk_size=disk_size
}



if (Annovar){
	call annovar.ANNOVAR as TNseq_ANNOVAR {
		input:
			vcf=TNseq_bcftools.norm_vcf,
			annovar_database=annovar_database,
			docker=docker_annovar,
			cluster_config=cluster_config,
			disk_size=disk_size
  }

    call tmb.TMB as TMB{
        input:
            sample=sample_id,
            hg38_CDS=hg38_CDS,
            regions=regions,
            snpindel_txt=TNseq_ANNOVAR.multianno_txt,
            docker=docker_tmb,
            cluster_config="OnDemand bcs.ps.g.large img-ubuntu-vpc",
            disk_size=disk_size,
            AF_filter=AF_filter
    }

    call annovar.ANNOVAR as Haplotyper_ANNOVAR {
		input:
			vcf=Haplotyper_bcftools.norm_vcf,
			annovar_database=annovar_database,
			docker=docker_annovar,
			cluster_config=cluster_config,
			disk_size=disk_size
  	}
}
}