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Update paths for Azure in reference tsv files and example json #181

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patmagee opened this issue Jan 23, 2025 · 0 comments
Open

Update paths for Azure in reference tsv files and example json #181

patmagee opened this issue Jan 23, 2025 · 0 comments
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@patmagee
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Describe the bug

The latest versions of CoA do not allow you to mount public buckets with a SAS Url. Effectively, this means two things:

  1. The ref_map and tertiary_map files refer to paths that will not be usable within a CoA workflow
  2. The *.input.json files reference the wrong path
  3. Importantly DO NOT mount the /datasetpbrarediseases/dataset/ container in either the externalContainer or externalSaSContainer section in the AksValues.yaml

Details

  1. Update /datasetpbrarediseases/dataset/ to be https://datasetpbrarediseases.blob.core.windows.net/dataset/ for all resources and have microsoft update the ref_map / tertiary_map in the public bucket
  2. Update the inputs files
{
  "humanwgs_family.family": {
    "family_id": "String",
    "samples": [
      {
        "sample_id": "String",
        "hifi_reads": [
          "File"
        ],
        "affected": "Boolean",
        "sex": "String? (optional, ['MALE', 'FEMALE', null])",
        "father_id": "String? (optional)",
        "mother_id": "String? (optional)"
      }
    ]
  },
  "humanwgs_family.phenotypes": "String? (optional)",
  "humanwgs_family.ref_map_file": "https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v2.0.0/GRCh38.ref_map.v2p0p0.azure.tsv",
  "humanwgs_family.tertiary_map_file": "https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v2.0.0/GRCh38.tertiary_map.v2p0p0.azure.tsv",
  "humanwgs_family.backend": "Azure",
  "humanwgs_family.preemptible": "Boolean"
}
@patmagee patmagee added the bug Something isn't working label Jan 23, 2025
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