Test xml_variant_ingestion workflow with new test data from MONSTAR

icgc-argo / workflow-roadmap

Roadmap and management for genomic data processing

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Test xml_variant_ingestion workflow with new test data from MONSTAR #455

Open guanqiaofeng opened 2 weeks ago

guanqiaofeng commented 2 weeks ago

| short-variants | copy-number-alterations | rearrangements -- | -- | -- | -- ORD-0000001-01.xml | Y | Y | ORD-0000002-01.xml | Y | | ORD-0000003-01.xml | Y | | ORD-0000004-01.xml | Y | | ORD-0000005-01.xml | Y | Y | Y

guanqiaofeng commented 2 weeks ago

[x] Need to test current workflow run properly for short-variants and rearrangements

[x] Need to extend workflow for copy-number-alterations
[x] Need to add flexibility in workflow to handle different types of variation provided by file

guanqiaofeng commented 1 week ago

https://github.com/icgc-argo-workflows/xml_variant_ingestion/pull/3