variant-calling/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/TNscope.wdl" as TNscope
import "./tasks/somatic.wdl" as somatic
import "./tasks/processSomatic.wdl" as processSomatic
import "./tasks/somaticFilter.wdl" as somaticFilter
import "./tasks/ANNOVAR.wdl" as ANNOVAR
import "./tasks/VEP.wdl" as VEP


workflow {{ project_name }} {
  
  String sample_id
  File? tumor_fastq_1
  File? tumor_fastq_2
  File? normal_fastq_1
  File? normal_fastq_2
  File? tumor_deduped_bam
  File? tumor_deduped_bam_index
  File? normal_deduped_bam
  File? normal_deduped_bam_index

  String SENTIEON_INSTALL_DIR
  String SENTIEON_LICENSE
  String sentieon_docker
  String varscan_docker
  String annovar_docker
  String vep_docker

  File ref_dir
  String fasta
  File dbmills_dir
  String db_mills
  File dbsnp_dir
  String dbsnp
  File germline_resource
  File germline_resource_tbi
  String hg
  File annovar_database
  
  File? regions
  Int? interval_padding
  File? tnseq_pon
  File? tnscope_pon

  String vep_path
  File cache
  String species
  String vcf2maf_path

  String disk_size
  String cluster_config

  Boolean haplotyper
  Boolean tnseq
  Boolean tnscope
  Boolean varscan

  Boolean annovar
  Boolean vep
  Boolean only_pass

  if (tumor_fastq_1!= "") {
    call mapping.mapping as tumor_mapping {
      input: 
      group=sample_id + '_tumor',
      sample=sample_id + '_tumor',
      fastq_1=tumor_fastq_1,
      fastq_2=tumor_fastq_2,
      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
      SENTIEON_LICENSE=SENTIEON_LICENSE,
      pl="ILLUMINAL",
      fasta=fasta,
      ref_dir=ref_dir,
      docker=sentieon_docker,
      disk_size=disk_size,
      cluster_config=cluster_config
    }

    call Metrics.Metrics as tumor_Metrics {
      input:
      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
      SENTIEON_LICENSE=SENTIEON_LICENSE,
      fasta=fasta,
      ref_dir=ref_dir,
      sorted_bam=tumor_mapping.sorted_bam,
      sorted_bam_index=tumor_mapping.sorted_bam_index,
      sample=sample_id + '_tumor',
      docker=sentieon_docker,
      disk_size=disk_size,
      cluster_config=cluster_config
    }

    call Dedup.Dedup as tumor_Dedup {
      input:
      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
      SENTIEON_LICENSE=SENTIEON_LICENSE,
      sorted_bam=tumor_mapping.sorted_bam,
      sorted_bam_index=tumor_mapping.sorted_bam_index,
      sample=sample_id + '_tumor',
      docker=sentieon_docker,
      disk_size=disk_size,
      cluster_config=cluster_config
    }

    call deduped_Metrics.deduped_Metrics as tumor_deduped_Metrics {
      input:
      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
      SENTIEON_LICENSE=SENTIEON_LICENSE,
      fasta=fasta,
      ref_dir=ref_dir,
      deduped_bam=tumor_Dedup.deduped_bam,
      deduped_bam_index=tumor_Dedup.deduped_bam_index,
      sample=sample_id + '_tumor',
      docker=sentieon_docker,
      disk_size=disk_size,
      cluster_config=cluster_config
    }

    call BQSR.BQSR as tumor_BQSR {
      input:
      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
      SENTIEON_LICENSE=SENTIEON_LICENSE,
      fasta=fasta,
      ref_dir=ref_dir,
      deduped_bam=tumor_Dedup.deduped_bam,
      deduped_bam_index=tumor_Dedup.deduped_bam_index,
      db_mills=db_mills,
      dbmills_dir=dbmills_dir,
      dbsnp=dbsnp,
      dbsnp_dir=dbsnp_dir,
      sample=sample_id + '_tumor',
      docker=sentieon_docker,
      disk_size=disk_size,
      cluster_config=cluster_config
    }
  }

  if (tumor_deduped_bam != ""){
    call BQSR.BQSR as tumor_BQSR {
      input:
      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
      SENTIEON_LICENSE=SENTIEON_LICENSE,
      fasta=fasta,
      ref_dir=ref_dir,
      deduped_bam=tumor_deduped_bam,
      deduped_bam_index=tumor_deduped_bam_index,
      db_mills=db_mills,
      dbmills_dir=dbmills_dir,
      dbsnp=dbsnp,
      dbsnp_dir=dbsnp_dir,
      sample=sample_id + '_tumor',
      docker=sentieon_docker,
      disk_size=disk_size,
      cluster_config=cluster_config
    }
  }

  if (normal_fastq_1!= "") {
    call mapping.mapping as normal_mapping {
      input: 
      group=sample_id + '_normal',
      sample=sample_id + '_normal',
      fastq_1=normal_fastq_1,
      fastq_2=normal_fastq_2,
      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
      SENTIEON_LICENSE=SENTIEON_LICENSE,
      pl="ILLUMINAL",
      fasta=fasta,
      ref_dir=ref_dir,
      docker=sentieon_docker,
      disk_size=disk_size,
      cluster_config=cluster_config
    }

    call Metrics.Metrics as normal_Metrics {
      input:
      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
      SENTIEON_LICENSE=SENTIEON_LICENSE,
      fasta=fasta,
      ref_dir=ref_dir,
      sorted_bam=normal_mapping.sorted_bam,
      sorted_bam_index=normal_mapping.sorted_bam_index,
      sample=sample_id + '_normal',
      regions=regions,
      docker=sentieon_docker,
      disk_size=disk_size,
      cluster_config=cluster_config
    }

    call Dedup.Dedup as normal_Dedup {
      input:
      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
      SENTIEON_LICENSE=SENTIEON_LICENSE,
      sorted_bam=normal_mapping.sorted_bam,
      sorted_bam_index=normal_mapping.sorted_bam_index,
      sample=sample_id + '_normal',
      docker=sentieon_docker,
      disk_size=disk_size,
      cluster_config=cluster_config
    }

    call deduped_Metrics.deduped_Metrics as normal_deduped_Metrics {
      input:
      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
      SENTIEON_LICENSE=SENTIEON_LICENSE,
      fasta=fasta,
      ref_dir=ref_dir,
      deduped_bam=normal_Dedup.deduped_bam,
      deduped_bam_index=normal_Dedup.deduped_bam_index,
      sample=sample_id + '_normal',
      regions=regions,
      docker=sentieon_docker,
      disk_size=disk_size,
      cluster_config=cluster_config
    }

    call BQSR.BQSR as normal_BQSR {
      input:
      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
      SENTIEON_LICENSE=SENTIEON_LICENSE,
      fasta=fasta,
      ref_dir=ref_dir,
      deduped_bam=normal_Dedup.deduped_bam,
      deduped_bam_index=normal_Dedup.deduped_bam_index,
      db_mills=db_mills,
      dbmills_dir=dbmills_dir,
      dbsnp=dbsnp,
      dbsnp_dir=dbsnp_dir,
      sample=sample_id + '_normal',
      docker=sentieon_docker,
      disk_size=disk_size,
      cluster_config=cluster_config
    }
  }

  if (normal_deduped_bam != ""){
    call BQSR.BQSR as normal_BQSR {
      input:
      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
      SENTIEON_LICENSE=SENTIEON_LICENSE,
      fasta=fasta,
      ref_dir=ref_dir,
      deduped_bam=normal_deduped_bam,
      deduped_bam_index=normal_deduped_bam_index,
      db_mills=db_mills,
      dbmills_dir=dbmills_dir,
      dbsnp=dbsnp,
      dbsnp_dir=dbsnp_dir,
      sample=sample_id + '_normal',
      docker=sentieon_docker,
      disk_size=disk_size,
      cluster_config=cluster_config
    }
  }

  if (haplotyper) {
    call Haplotyper.Haplotyper as Haplotyper {
      input:
      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
      SENTIEON_LICENSE=SENTIEON_LICENSE,
      sample=sample_id + '_normal',
      fasta=fasta,
      ref_dir=ref_dir,
      deduped_bam=normal_Dedup.deduped_bam,
      deduped_bam_index=normal_Dedup.deduped_bam_index,
      recal_table=normal_BQSR.recal_table,
      dbsnp=dbsnp,
      dbsnp_dir=dbsnp_dir,
      regions=regions,
      docker=sentieon_docker,
      disk_size=disk_size,
      cluster_config=cluster_config
    }
  }
  
  if (tnseq) {
    call TNseq.TNseq as TNseq {
      input:
      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
      SENTIEON_LICENSE=SENTIEON_LICENSE,
      sample=sample_id,
      normal_deduped_bam=normal_Dedup.deduped_bam,
      normal_deduped_bam_index=normal_Dedup.deduped_bam_index,
      normal_recal_table=normal_BQSR.recal_table,
      tumor_deduped_bam=tumor_Dedup.deduped_bam,
      tumor_deduped_bam_index=tumor_Dedup.deduped_bam_index,
      tumor_recal_table=tumor_BQSR.recal_table,
      normal_name=sample_id + "_normal",
      tumor_name=sample_id + "_tumor",
      fasta=fasta,
      ref_dir=ref_dir,
      regions=regions,
      interval_padding=interval_padding,
      germline_resource=germline_resource,
      germline_resource_tbi=germline_resource_tbi,
      pon_vcf=tnseq_pon,
      docker=sentieon_docker,
      cluster_config=cluster_config,
      disk_size=disk_size
    }

    if (annovar) {
      call ANNOVAR.ANNOVAR as TNseq_annovar {
        input:
        vcf=TNseq.TNseq_vcf,
        hg=hg,
        only_pass=only_pass,
        annovar_database=annovar_database,
        docker=annovar_docker,
        cluster_config=cluster_config,
        disk_size=disk_size
      }
    }

    if (vep) {
      call VEP.VEP as TNseq_VEP {
        input: 
        vcf=TNseq.TNseq_vcf,
        hg=hg,
        only_pass=only_pass,
        sample_id=sample_id,
        tumor_id=sample_id + "_tumor",
        normal_id=sample_id + "_normal",
        ref_dir=ref_dir,
        fasta=fasta,
        vep_path=vep_path,
        cache=cache,
        species=species,
        vcf2maf_path=vcf2maf_path,
        docker=vep_docker,
        cluster_config=cluster_config,
        disk_size=disk_size
      }
    }
  }

  if (tnscope) {
    call TNscope.TNscope as TNscope {
      input:
      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
      SENTIEON_LICENSE=SENTIEON_LICENSE,
      sample=sample_id,
      normal_deduped_bam=normal_Dedup.deduped_bam,
      normal_deduped_bam_index=normal_Dedup.deduped_bam_index,
      normal_recal_table=normal_BQSR.recal_table,
      tumor_deduped_bam=tumor_Dedup.deduped_bam,
      tumor_deduped_bam_index=tumor_Dedup.deduped_bam_index,
      tumor_recal_table=tumor_BQSR.recal_table,
      normal_name=sample_id + "_normal",
      tumor_name=sample_id + "_tumor",
      fasta=fasta,
      ref_dir=ref_dir,
      regions=regions,
      interval_padding=interval_padding,
      dbsnp=dbsnp,
      dbsnp_dir=dbsnp_dir,
      pon_vcf=tnscope_pon,
      docker=sentieon_docker,
      cluster_config=cluster_config,
      disk_size=disk_size
    }
    
    if (annovar) {
      call ANNOVAR.ANNOVAR as TNscope_annovar {
        input:
        vcf=TNscope.TNscope_vcf,
        hg=hg,
        only_pass=only_pass,
        annovar_database=annovar_database,
        docker=annovar_docker,
        cluster_config=cluster_config,
        disk_size=disk_size
      }
    }

    if (vep) {
      call VEP.VEP as TNscope_VEP {
        input: 
        vcf=TNscope.TNscope_vcf,
        hg=hg,
        only_pass=only_pass,
        sample_id=sample_id,
        tumor_id=sample_id + "_tumor",
        normal_id=sample_id + "_normal",
        ref_dir=ref_dir,
        fasta=fasta,
        vep_path=vep_path,
        cache=cache,
        species=species,
        vcf2maf_path=vcf2maf_path,
        docker=vep_docker,
        cluster_config=cluster_config,
        disk_size=disk_size
      }
    }
  }

  if (varscan) {
    call somatic.somatic as somatic {
      input:
      sample=sample_id,
      tumor_bam=tumor_Dedup.deduped_bam,
      tumor_bam_index=tumor_Dedup.deduped_bam_index,
      normal_bam=normal_Dedup.deduped_bam,
      normal_bam_index=normal_Dedup.deduped_bam_index,
      ref_dir=ref_dir,
      fasta=fasta,    
      docker=varscan_docker,
      disk_size=disk_size,
      cluster_config=cluster_config
    }

    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_config
    }

    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_config
    }

    if (annovar) {
      call ANNOVAR.ANNOVAR as VarScan_annovar {
        input:
        vcf=somaticFilter.varscan_somatic_filter,
        hg=hg,
        only_pass=only_pass,
        annovar_database=annovar_database,
        docker=annovar_docker,
        cluster_config=cluster_config,
        disk_size=disk_size
      }
    }

    if (vep) {
      call VEP.VEP as VarScan_VEP {
        input: 
        vcf=VarScan.VarScan_vcf,
        hg=hg,
        only_pass=only_pass,
        sample_id=sample_id,
        tumor_id=sample_id + "_tumor",
        normal_id=sample_id + "_normal",
        ref_dir=ref_dir,
        fasta=fasta,
        vep_path=vep_path,
        cache=cache,
        species=species,
        vcf2maf_path=vcf2maf_path,
        docker=vep_docker,
        cluster_config=cluster_config,
        disk_size=disk_size
      }
    }
  }
}