caller-test/workflow.wdl

import "./tasks/TNseq.wdl" as TNseq
import "./tasks/TNseqold.wdl" as TNseqold
import "./tasks/TNscope.wdl" as TNscope
import "./tasks/annovar.wdl" as annovar

workflow {{ project_name }} {
  
  String sample_id
  File? tumor_bam
  File? tumor_bai
  File? tumor_table
  File? normal_bam
  File? normal_bai
  File? normal_table

  File? corealigner_bam
  File? corealigner_bai

  String SENTIEON_INSTALL_DIR
  String SENTIEON_LICENSE
  String sentieon_docker
  String varscan_docker
  String annovar_docker
  String maftools_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? regions
  Int? interval_padding

  File database
  String disk_size
  String cluster_config

  File? tnseq_pon
  File? tnscope_pon
  File? cosmic_dir
  String? cosmic_vcf

  Boolean germline
  Boolean tnseq
  Boolean tnseqold
  Boolean tnscope
  Boolean varscan

  if (tnseqold) {
    call TNseqold.TNseqold as TNseqold {
      input:
      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
      SENTIEON_LICENSE=SENTIEON_LICENSE,
      sample=sample_id,
      corealigner_bam=corealigner_bam,
      corealigner_bai=corealigner_bai,
      normal_name=sample_id + "_normal",
      tumor_name=sample_id + "_tumor",
      fasta=fasta,
      ref_dir=ref_dir,
      regions=regions,
      dbsnp=dbsnp,
      dbsnp_dir=dbsnp_dir,
      interval_padding=interval_padding,
      pon_vcf=tnseq_pon,
      docker=sentieon_docker,
      cluster_config=cluster_config,
      disk_size=disk_size
    }

    call annovar.annovar as TNseqold_annovar {
    input:
      sample=sample_id,
      vcf=TNseqold.TNseq_vcf,
      database=database,
      docker=annovar_docker,
      cluster_config=cluster_config,
      disk_size=disk_size
    }
  }

  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_bam,
      normal_recaled_bam_index=normal_bai,
      normal_recal_table=normal_table,
      tumor_recaled_bam=tumor_bam,
      tumor_recaled_bam_index=tumor_bai,
      tumor_recal_table=tumor_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_bam,
      normal_recaled_bam_index=normal_bai,
      normal_recal_table=normal_table,
      tumor_recaled_bam=tumor_bam,
      tumor_recaled_bam_index=tumor_bai,
      tumor_recal_table=tumor_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
    }
  }
}