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Added support for TSO BAM fingerprinting through Holmes #566

Merged
merged 2 commits into from
Feb 28, 2023
Merged

Added support for TSO BAM fingerprinting through Holmes #566

merged 2 commits into from
Feb 28, 2023

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victorskl
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@victorskl victorskl commented Feb 28, 2023 •
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  • Refactored to improve Holmes payload with HolmesDto model
  • Re-enabled somalier extract step for TSO workflow in orchestrator
    as upstream #153 is resolved
  • Updated somalier extract step to use reference hg19 for TSO BAM
  • Dropped somalier endpoint - UI to use direct Lambda call

Fixes #509

@victorskl
Added support for TSO BAM fingerprinting through Holmes
f071b23 
* Refactored to improve Holmes payload with HolmesDto model
* Re-enabled somalier extract step for TSO workflow in orchestrator
  as upstream #153 is resolved
* Updated somalier extract step to use reference hg19 for TSO BAM
* Dropped somalier endpoint - UI to use direct Lambda call

Fixes #509
@victorskl victorskl self-assigned this Feb 28, 2023
@victorskl victorskl added the feature New feature label Feb 28, 2023
@victorskl victorskl added this to the Release 2.1 milestone Feb 28, 2023
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@reisingerf @williamputraintan FYI, review if any

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Thanks all for review. Merging...

@victorskl victorskl merged commit 98aab3f into dev Feb 28, 2023
@victorskl victorskl deleted the support-tso-bam-fingerprint-holmes branch February 28, 2023 23:32
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@alexiswl alexiswl alexiswl approved these changes

@andrewpatto andrewpatto andrewpatto approved these changes

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@victorskl victorskl

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Successfully merging this pull request may close these issues.

Add SOMALIER_EXTRACT_STEP to ctTSO500 BAMs for the Holmes pipeline
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@victorskl @andrewpatto @alexiswl