{
  "reference_sequence": {
    "path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz",
    "class": "File"
  },
  "write_qc": true,
  "reference_sequence_index": {
    "path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz.fai",
    "class": "File"
  },
  "input_vcf": {
    "path": "https://raw.githubusercontent.com/CancerCollaboratory/dockstore-tool-snpeff/1.0/ALL.chrX.BI_Beagle.20100804.sites.vcf",
    "class": "File"
  },
  "input_bam": {
    "path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/data_for_testing/HCC1143_ds/HCC1143.bam",
    "class": "File"
  },
  "input_bam_index": {
    "path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/data_for_testing/HCC1143_ds/HCC1143.bam.bai",
    "class": "File"
  },
  "output_vcf_file": {
    "path": "example_output_directory/output.vcf",
    "class": "File"
  }
}