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New expedited document type for genomic workflow output data #492

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3 tasks done
Tracked by #491
znatty22 opened this issue Oct 22, 2020 · 1 comment · Fixed by #494
Closed
3 tasks done
Tracked by #491

New expedited document type for genomic workflow output data #492

znatty22 opened this issue Oct 22, 2020 · 1 comment · Fixed by #494
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@znatty22
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znatty22 commented Oct 22, 2020

We need to add a new expedited document type to capture the genomic workflow output manifest produced by the Bix team after they run the genomic workflows on the source sequencing files within a Study. This manifest will be used by the ingest job to register the harmonized genomic files and link them to their specimens and sequencing experiments in the Dataservice.

The current manifest format is a JSON file that looks like: https://datatracker.kidsfirstdrc.org/study/SD_8Y99QZJJ/documents/SF_KQZ9MMH6

We would like to change this format to a tabular format so that no additional changes are needed on Data Tracker.

To Do

  • Verify with Bix that the name "Genomic Workflow Output Manifest" accurately represents the concept
  • Design the desired tabular format for the Genomic Workflow Output Manifest and get it approved by Bix
  • Add functionality to Study Creator API for new expedited type: Genomic Workflow Output Manifest
@znatty22 znatty22 added the feature New functionality label Oct 22, 2020
@znatty22 znatty22 self-assigned this Oct 22, 2020
@znatty22 znatty22 changed the title New expedited document for genomic workflow output data New expedited document type for genomic workflow output data Oct 22, 2020
@znatty22
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znatty22 commented Oct 26, 2020

See sample manifest in new format (GH forces us to use .txt when attaching files to comments, but this will be .tsv in production use):
sample_genomic_workflow_output_manifest.txt

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