Clinical-Genomics / hermes

Communication layer between CG and the pipelines.
https://clinical-genomics.github.io/hermes/
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Add Gens files for Balsamic WGS analysis #86

Closed ivadym closed 8 months ago

ivadym commented 10 months ago

Description

Storing Gens coverage and baf files since we'll start uploading Balsamic WGS cases to Gens: https://github.com/Clinical-Genomics/cg/issues/2447.

How to prepare for test

How to test

Expected test outcome

Review

This version is a

Implementation Plan

mathiasbio commented 10 months ago

Starting this review now : )

codecov-commenter commented 10 months ago

Codecov Report

Attention: 6 lines in your changes are missing coverage. Please review.

Comparison is base (a51aefb) 89.83% compared to head (655199a) 90.16%. Report is 6 commits behind head on main.

Files Patch % Lines
cg_hermes/cli/validate.py 80.95% 4 Missing :warning:
cg_hermes/cli/common.py 33.33% 2 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #86 +/- ## ========================================== + Coverage 89.83% 90.16% +0.32% ========================================== Files 24 25 +1 Lines 541 559 +18 ========================================== + Hits 486 504 +18 Misses 55 55 ``` | [Flag](https://app.codecov.io/gh/Clinical-Genomics/hermes/pull/86/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Clinical-Genomics) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/Clinical-Genomics/hermes/pull/86/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Clinical-Genomics) | `90.16% <89.47%> (+0.32%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Clinical-Genomics#carryforward-flags-in-the-pull-request-comment) to find out more.

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ivadym commented 8 months ago

Deployed:

Screenshot 2024-01-22 at 10 07 04