#!/usr/bin/env cwl-runner
cwl:tool: detect_variants.cwl
reference:
  class: File
  path: GRCh38_full_analysis_set_plus_decoy_hla.fa
interval_list:
  class: File
  path: xgen-exome-research-panel-targets.interval_list
dbsnp_vcf:
  class: File
  path: Homo_sapiens_assembly38.dbsnp138.vcf.gz
cosmic_vcf:
  class: File
  path: Cosmic_v79.dictsorted.vcf.gz
normal_cram: 
  class: File
  path: H_NJ-HCC1395-HCC1395_BL_exome.cram
tumor_cram:
  class: File
  path: H_NJ-HCC1395-HCC1395_exome.cram
strelka_exome_mode: true
vep_cache_dir:
  class: File
  path: vep_cache_location.txt
synonyms_file:
  class: File
  path: chromAlias.ensembl.txt

#!/usr/bin/env cwl-runner
reference:
  class: File
  path: GRCh38_full_analysis_set_plus_decoy_hla.fa
interval_list:
  class: File
  path: xgen-exome-research-panel-targets.interval_list
dbsnp_vcf:
  class: File
  path: Homo_sapiens_assembly38.dbsnp138.vcf.gz
cosmic_vcf:
  class: File
  path: Cosmic_v79.dictsorted.vcf.gz
normal_cram: 
  class: File
  path: H_NJ-HCC1395-HCC1395_BL_exome.cram
tumor_cram:
  class: File
  path: H_NJ-HCC1395-HCC1395_exome.cram
strelka_exome_mode: true
vep_cache_dir:
  class: File
  path: vep_cache_location.txt
synonyms_file:
  class: File
  path: chromAlias.ensembl.txt
docm_vcf:
  class: File
  path: DoCM.hs37_011117_sanitized_sort_new_LiftOver_hg19ToHg38.vcf.gz

Remove cwl:tool line since schema is missing in toil. Add DoCM VCF file.
Remove cwl:tool line since schema is missing in toil. Add DoCM VCF file.
