WesPipe-hg19-bam/workflow.wdl

import "./tasks/mapping.wdl" as mapping
import "./tasks/Metrics.wdl" as Metrics
import "./tasks/Dedup.wdl" as Dedup
import "./tasks/deduped_Metrics.wdl" as deduped_Metrics
import "./tasks/BQSR.wdl" as BQSR
import "./tasks/Haplotyper.wdl" as Haplotyper
import "./tasks/TNseq.wdl" as TNseq
import "./tasks/bcftools.wdl" as bcftools
import "./tasks/ANNOVAR.wdl" as ANNOVAR
import "./tasks/Manta.wdl" as Manta
import "./tasks/AnnotSV.wdl" as AnnotSV
import "./tasks/CNVkit.wdl" as CNVkit
import "./tasks/MSIsensor.wdl" as MSIsensor
import "./tasks/HRD.wdl" as HRD
import "./tasks/TMB.wdl" as TMB

import "./tasks/fastqc.wdl" as fastqc
import "./tasks/fastqscreen.wdl" as fastqscreen
import "./tasks/qualimap.wdl" as qualimap

import "./tasks/TNscope.wdl" as TNscope
import "./tasks/somatic.wdl" as somatic
import "./tasks/processSomatic.wdl" as processSomatic
import "./tasks/somaticFilter.wdl" as somaticFilter

workflow {{ project_name }} {
  
  String sample_id
  File? tumor_bam
  File? tumor_bam_index
  File? normal_bam
  File? normal_bam_index
  String? duplex_umi
  String? read_structure
  
  String SENTIEON_LICENSE
  String sentieon_docker
  String manta_docker
  String bcftools_docker
  String annovar_docker
  String annotsv_docker
  String cnvkit_docker
  String sequenza_docker
  String msisensor_docker
  String tmb_docker
  
  String platform
  File ref_dir
  String fasta
  File dbmills_dir
  String db_mills
  File dbsnp_dir
  String dbsnp
  File germline_resource
  File germline_resource_tbi
  File annovar_database
  File annotsv_database
  File gc
  File baseline
  File ref_flat
  
  File? regions
  Int? interval_padding
  
  String disk_size
  String cluster_2cpu_4gb
  String cluster_16cpu_32gb
  
  Boolean qc
  String fastqc_docker
  String fastqscreen_docker
  String qualimap_docker
  File screen_ref_dir
  File fastq_screen_conf

  Boolean multi_caller
  String varscan_docker

  call TNseq.TNseq as TNseq {
    input:
    SENTIEON_LICENSE=SENTIEON_LICENSE,
    sample=sample_id,
    normal_bam=normal_bam,
    normal_bam_index=normal_bam_index,
    tumor_bam=tumor_bam,
    tumor_bam_index=tumor_bam_index,
    normal_name=sample_id + ".N",
    tumor_name=sample_id + ".T",
    fasta=fasta,
    ref_dir=ref_dir,
    dbsnp=dbsnp,
    dbsnp_dir=dbsnp_dir,
    regions=regions,
    interval_padding=interval_padding,
    germline_resource=germline_resource,
    germline_resource_tbi=germline_resource_tbi,
    docker=sentieon_docker,
    cluster_config=cluster_16cpu_32gb,
    disk_size=disk_size
  }
  
  call bcftools.bcftools as TNseq_bcftools {
    input:
    vcf=TNseq.vcf,
    fasta=fasta,
    ref_dir=ref_dir,
    docker=bcftools_docker,
    cluster_config=cluster_2cpu_4gb,
    disk_size=disk_size
  }
  
  call ANNOVAR.ANNOVAR as TNseq_ANNOVAR {
    input:
    vcf=TNseq_bcftools.norm_vcf,
    annovar_database=annovar_database,
    docker=annovar_docker,
    cluster_config=cluster_16cpu_32gb,
    disk_size=disk_size
  }
  
  if (multi_caller){
    call somatic.somatic as somatic {
      input:
      sample=sample_id,
      normal_bam=normal_bam,
      normal_bam_index=normal_bam_index,
      tumor_bam=tumor_bam,
      tumor_bam_index=tumor_bam_index,
      ref_dir=ref_dir,
      fasta=fasta,
      docker=varscan_docker,
      disk_size=disk_size,
      cluster_config=cluster_16cpu_32gb
    }
    
    call processSomatic.processSomatic as processSomatic {
      input:
      sample=sample_id,
      varscan_snp=somatic.varscan_snp,
      varscan_indel=somatic.varscan_indel,
      docker=varscan_docker,
      disk_size=disk_size,
      cluster_config=cluster_16cpu_32gb
    }
    
    call somaticFilter.somaticFilter as somaticFilter {
      input:
      sample=sample_id,
      varscan_snp_somatic_hc=processSomatic.varscan_snp_somatic_hc,
      varscan_snp_germline_hc=processSomatic.varscan_snp_germline_hc,
      varscan_snp_loh_hc=processSomatic.varscan_snp_loh_hc,
      varscan_indel_somatic_hc=processSomatic.varscan_indel_somatic_hc,
      varscan_indel_germline_hc=processSomatic.varscan_indel_germline_hc,
      varscan_indel_loh_hc=processSomatic.varscan_indel_loh_hc,
      varscan_indel=somatic.varscan_indel,
      docker=varscan_docker,
      disk_size=disk_size,
      cluster_config=cluster_16cpu_32gb
    }
    
    call bcftools.bcftools as VarScan_bcftools {
      input:
      vcf=somaticFilter.varscan_somatic_filter,
      fasta=fasta,
      ref_dir=ref_dir,
      docker=bcftools_docker,
      cluster_config=cluster_2cpu_4gb,
      disk_size=disk_size
    }
    
    call ANNOVAR.ANNOVAR as VarScan_ANNOVAR {
      input:
      vcf=VarScan_bcftools.norm_vcf,
      annovar_database=annovar_database,
      docker=annovar_docker,
      cluster_config=cluster_16cpu_32gb,
      disk_size=disk_size
    }
    
    call TNscope.TNscope as TNscope {
      input:
      SENTIEON_LICENSE=SENTIEON_LICENSE,
      sample=sample_id,
      normal_recaled_bam=normal_bam,
      normal_recaled_bam_index=normal_bam_index,
      tumor_recaled_bam=tumor_bam,
      tumor_recaled_bam_index=tumor_bam_index,
      normal_name=sample_id + ".N",
      tumor_name=sample_id + ".T",
      fasta=fasta,
      ref_dir=ref_dir,
      regions=regions,
      interval_padding=interval_padding,
      dbsnp=dbsnp,
      dbsnp_dir=dbsnp_dir,
      docker=sentieon_docker,
      cluster_config=cluster_16cpu_32gb,
      disk_size=disk_size
    }
    
    call bcftools.bcftools as TNscope_bcftools {
      input:
      vcf=TNscope.TNscope_vcf,
      fasta=fasta,
      ref_dir=ref_dir,
      docker=bcftools_docker,
      cluster_config=cluster_2cpu_4gb,
      disk_size=disk_size
    }
    
    call ANNOVAR.ANNOVAR as TNscope_ANNOVAR {
      input:
      vcf=TNscope_bcftools.norm_vcf,
      annovar_database=annovar_database,
      docker=annovar_docker,
      cluster_config=cluster_16cpu_32gb,
      disk_size=disk_size
    }
  }
}