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Update seq-tools to support nested CRAM info check #40

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edsu7 opened this issue Oct 13, 2022 · 2 comments
Closed
3 tasks

Update seq-tools to support nested CRAM info check #40

edsu7 opened this issue Oct 13, 2022 · 2 comments
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@edsu7
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edsu7 commented Oct 13, 2022

Given the example :

  "files": [
    {
      "fileName": "anon_chr1_completeA.bam",
      "fileSize": 269442,
      "fileMd5sum": "968711f781f217dfb1de630e520ccacb",
      "fileType": "BAM",
      "fileAccess": "controlled",
      "dataType": "Submitted Reads",
      "info": {
        "data_category": "Sequencing Reads",
        "original_cram_info": {
          "fileName": "anon_chr1_completeA.cram",
          "fileSize": 132507,
          "fileMd5sum": "0d1776d44d8da87758d6b159aa8e6bc5",
          "fileType": "CRAM",
          "referenceFileName": "hs73d5.fa.gz"
        }
      }
    }

Seq-tools currently only checks files[0][fileSize] and files[0][fileMd5sum].
For CRAM files that have their original info nested and converted version is auto-populates files[0][fileSize] and files[0][fileMd5sum] .
This potentially allows a submitter to submit incorrect CRAM info and bypass md5sum and fileSize checks.

  • Update Seq-tools
  • Release updated seq-tools version
  • Update Seq-tools WFPM module
@puneet-oicr
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All PRs approved. Merge to Seq-Tools pending next

@b-f-chan
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Merged, closing

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