Dockstore.json

{
  "run-id": "run_id",
  "tumor-bam":
  {
    "path":"https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/data_for_testing/HCC1143_ds/HCC1143.bam",
    "class":"File"
  },
  "normal-bam":
  {
    "path":"https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/data_for_testing/HCC1143_ds/HCC1143_BL.bam",
    "class":"File"
  },
  "reference-gz":
  {
    "path": "https://dcc.icgc.org/api/v1/download?fn=/PCAWG/reference_data/pcawg-dkfz/dkfz-workflow-dependencies_150318_0951.tar.gz",
    "class": "File"
  },
  "delly-bedpe":
  {
    "path":"https://raw.githubusercontent.com/ICGC-TCGA-PanCancer/dkfz_dockered_workflows/2.0.0_cwl1.0/run_id.embl-delly_1-3-0-preFilter.20150318.somatic.sv.bedpe.txt",
    "class":"File"
  },
  "germline_indel_vcf_gz": {
    "path": "/media/large_volume/output/germline.indel.vcf.gz",
    "class": "File"
  },
  "somatic_snv_mnv_vcf_gz": {
    "path": "/media/large_volume/output/somatic.snv.mnv.vcf.gz",
    "class": "File"
  },
  "germline_snv_mnv_vcf_gz": {
    "path": "/media/large_volume/output/germline.snv.mnv.vcf.gz",
    "class": "File"
  },
  "somatic_cnv_tar_gz": {
    "path": "/media/large_volume/output/somatic.cnv.tar.gz",
    "class": "File"
  },
  "somatic_cnv_vcf_gz": {
    "path": "/media/large_volume/output/somatic.cnv.vcf.gz",
    "class": "File"
  },
  "somatic_indel_tar_gz": {
    "path": "/media/large_volume/output/somatic.indel.tar.gz",
    "class": "File"
  },
  "somatic_snv_mnv_tar_gz": {
    "path": "/media/large_volume/output/somatic.snv.mnv.tar.gz",
    "class": "File"
  },
  "somatic_indel_vcf_gz": {
    "path": "/media/large_volume/output/somatic.indel.vcf.gz",
    "class": "File"
  }
}