Dockstore_cwl.json

{
  "reads": [
  {
  "path":"https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/data_for_testing/hg19.chr22.5x.normal.bam",
  "basename": "hg19.chr22.5x.normal.bam",
  "class":"File"
  },
  {"path":"https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/data_for_testing/hg19.chr22.5x.normal2.bam",
   "basename": "hg19.chr22.5x.normal2.bam",
  "class":"File"
  }
  ],
  "output_dir": "datastore",
  "output_file_basename": "hg19.chr22.5x.normal",
  "download_reference_files": "true",
  "reference_gz_amb": {
    "path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz.64.amb",
    "basename": "genome.fa.gz.64.amb",
    "class": "File"
  },
  "reference_gz_sa": {
    "path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz.64.sa",
    "basename": "genome.fa.gz.64.sa",
    "class": "File"
  },
  "reference_gz_pac": {
    "path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz.64.pac",
    "basename": "genome.fa.gz.64.pac",
    "class": "File"
  },
  "reference_gz_ann": {
    "path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz.64.ann",
    "basename": "genome.fa.gz.64.ann",
    "class": "File"
  },
  "reference_gz_bwt": {
    "path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz.64.bwt",
    "basename": "genome.fa.gz.64.bwt",
    "class": "File"
  },
  "reference_gz_fai": {
    "path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz.fai",
    "basename": "genome.fa.gz.fai",
    "class": "File"
  },
  "reference_gz": {
    "path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-bwa-mem/genome.fa.gz",
    "basename": "genome.fa.gz",
    "class": "File"
  }
}