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/Realigner.wdl" as Realigner
import "./tasks/BQSR.wdl" as BQSR
import "./tasks/Haplotyper.wdl" as Haplotyper
import "./tasks/corealigner.wdl" as corealigner
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/vcf2maf.wdl" as vcf2maf


workflow {{ project_name }} {
  
  String sample_id
  File tumor_fastq_1
  File tumor_fastq_2
  File normal_fastq_1
  File normal_fastq_2

  String SENTIEON_INSTALL_DIR
  String SENTIEON_LICENSE
  String sentieon_docker
  String varscan_docker
  String annovar_docker

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

  String disk_size
  String cluster_config
  
  Boolean haplotyper
  Boolean tnseq
  Boolean tnscope
  Boolean varscan

  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,
      Dedup_bam=tumor_Dedup.Dedup_bam,
      Dedup_bam_index=tumor_Dedup.Dedup_bam_index,
      sample=sample_id + '_tumor',
      docker=sentieon_docker,
      disk_size=disk_size,
      cluster_config=cluster_config
    }

    call Realigner.Realigner as tumor_Realigner {
      input:
      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
      SENTIEON_LICENSE=SENTIEON_LICENSE,
      fasta=fasta,
      ref_dir=ref_dir,
      Dedup_bam=tumor_Dedup.Dedup_bam,
      Dedup_bam_index=tumor_Dedup.Dedup_bam_index,
      db_mills=db_mills,
      dbmills_dir=dbmills_dir,
      sample=sample_id + '_tumor',
      docker=sentieon_docker,
      disk_size=disk_size,
      regions=regions,
      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,
      realigned_bam=tumor_Realigner.realigner_bam,
      realigned_bam_index=tumor_Realigner.realigner_bam_index,
      db_mills=db_mills,
      dbmills_dir=dbmills_dir,
      dbsnp=dbsnp,
      dbsnp_dir=dbsnp_dir,
      sample=sample_id + '_tumor',
      regions=regions,
      docker=sentieon_docker,
      disk_size=disk_size,
      cluster_config=cluster_config
    }
  }

  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,
    Dedup_bam=normal_Dedup.Dedup_bam,
    Dedup_bam_index=normal_Dedup.Dedup_bam_index,
    sample=sample_id + '_normal',
    regions=regions,
    docker=sentieon_docker,
    disk_size=disk_size,
    cluster_config=cluster_config
  }

  call Realigner.Realigner as normal_Realigner {
    input:
    SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
    SENTIEON_LICENSE=SENTIEON_LICENSE,
    fasta=fasta,
    ref_dir=ref_dir,
    Dedup_bam=normal_Dedup.Dedup_bam,
    Dedup_bam_index=normal_Dedup.Dedup_bam_index,
    db_mills=db_mills,
    dbmills_dir=dbmills_dir,
    sample=sample_id + '_normal',
    docker=sentieon_docker,
    disk_size=disk_size,
    regions=regions,
    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,
    realigned_bam=normal_Realigner.realigner_bam,
    realigned_bam_index=normal_Realigner.realigner_bam_index,
    db_mills=db_mills,
    dbmills_dir=dbmills_dir,
    dbsnp=dbsnp,
    dbsnp_dir=dbsnp_dir,
    sample=sample_id + '_normal',
    regions=regions,
    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,
      recaled_bam=normal_BQSR.recaled_bam,
      recaled_bam_index=normal_BQSR.recaled_bam_index,
      recaled_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_recaled_bam=normal_BQSR.recaled_bam,
      normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
      normal_recal_table=normal_BQSR.recal_table,
      tumor_recaled_bam=tumor_BQSR.recaled_bam,
      tumor_recaled_bam_index=tumor_BQSR.recaled_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
    }

    call annovar.annovar as TNseq_annovar {
      input:
      sample=sample_id,
      vcf=TNseq.TNseq_vcf,
      database=database,
      docker=annovar_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_recaled_bam=normal_BQSR.recaled_bam,
      normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
      normal_recal_table=normal_BQSR.recal_table,
      tumor_recaled_bam=tumor_BQSR.recaled_bam,
      tumor_recaled_bam_index=tumor_BQSR.recaled_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
    }
    
    call annovar.annovar as TNscope_annovar {
      input:
      sample=sample_id,
      vcf=TNscope.TNscope_vcf,
      database=database,
      docker=annovar_docker,
      cluster_config=cluster_config,
      disk_size=disk_size
    }
  }

  if (varscan) {
    call somatic.somatic as somatic {
      input:
      sample=sample_id,
      tumor_bam=tumor_BQSR.recaled_bam,
      tumor_bam_index=tumor_BQSR.recaled_bam_index,
      normal_bam=normal_BQSR.recaled_bam,
      normal_bam_index=normal_BQSR.recaled_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
    }

    call annovar.annovar as snp_somatic_annovar {
      input: 
      sample=sample_id,
      vcf=somaticFilter.varscan_snp_somatic_filter,
      database=database,
      docker=annovar_docker,
      cluster_config=cluster_config,
      disk_size=disk_size
    }

    call vcf2maf.vcf2maf as snp_somatic_vcf2maf {
      input:
      sample=sample_id,
      multianno_txt=snp_somatic_annovar.multianno_txt,
      docker=maftools_docker,
      cluster_config=cluster_config,
      disk_size=disk_size
    }
    
    call annovar.annovar as snp_loh_annovar {
      input: 
      sample=sample_id,
      vcf=somaticFilter.varscan_snp_loh_filter,
      database=database,
      docker=annovar_docker,
      cluster_config=cluster_config,
      disk_size=disk_size
    }
    
    call annovar.annovar as indel_somatic_annovar {
      input: 
      sample=sample_id,
      vcf=somaticFilter.varscan_indel_somatic_filter,
      database=database,
      docker=annovar_docker,
      cluster_config=cluster_config,
      disk_size=disk_size
    }
    
    call annovar.annovar as indel_loh_annovar {
      input: 
      sample=sample_id,
      vcf=somaticFilter.varscan_indel_loh_filter,
      database=database,
      docker=annovar_docker,
      cluster_config=cluster_config,
      disk_size=disk_size
    }
    }
  }
}