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feat: add cadd container #1222

Merged
merged 13 commits into from
Aug 17, 2023
Merged

feat: add cadd container #1222

merged 13 commits into from
Aug 17, 2023

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khurrammaqbool
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@khurrammaqbool khurrammaqbool commented Aug 10, 2023 •
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This PR:

Added: CADD container.

Review and tests:

  • Tests pass
  • Code review
  • New code is executed and covered by tests, and test approve

@khurrammaqbool khurrammaqbool requested a review from a team August 10, 2023 11:14
@khurrammaqbool khurrammaqbool self-assigned this Aug 10, 2023
@khurrammaqbool khurrammaqbool linked an issue Aug 10, 2023 that may be closed by this pull request
CADD scores for SNVs and INDELs #1106
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codecov bot commented Aug 10, 2023 •
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Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (f2046f4) 99.42% compared to head (311166e) 99.42%.

Additional details and impacted files 
@@           Coverage Diff            @@
##           develop    #1222   +/-   ##
========================================
  Coverage    99.42%   99.42%           
========================================
  Files           41       41           
  Lines         1916     1918    +2     
========================================
+ Hits          1905     1907    +2     
  Misses          11       11
Flag Coverage Δ
unittests 99.42% <100.00%> (+<0.01%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Changed Coverage Δ
BALSAMIC/utils/scheduler.py 100.00% <ø> (ø)
BALSAMIC/constants/analysis.py 100.00% <100.00%> (ø)
BALSAMIC/constants/cache.py 100.00% <100.00%> (ø)

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@khurrammaqbool khurrammaqbool mentioned this pull request Aug 11, 2023
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@khurrammaqbool khurrammaqbool force-pushed the feat/add_cadd_container branch from b8bd7a9 to 232b283 Compare August 11, 2023 12:50
mathiasbio
mathiasbio approved these changes Aug 14, 2023
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Nice job!
🔥 🧙 🔥
Protocol demands I ask thee: hath thee tested building and using the container?

ivadym
ivadym reviewed Aug 14, 2023
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Nice ⭐ Loving this new containers style

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ivadym
ivadym approved these changes Aug 16, 2023
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🥳 🥳

@khurrammaqbool
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Nice job! 🔥 🧙 🔥 Protocol demands I ask thee: hath thee tested building and using the container?

The tests for container pass and also the container is annotating CADD scores. More tests will be possible after adding the annotation in BALSAMIC workflow.

@sonarqubecloud
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Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

ivadym
ivadym approved these changes Aug 17, 2023
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Looks fine after pulling develop, go ahead with the merging 🎄 🎅

@khurrammaqbool khurrammaqbool merged commit a6445b4 into develop Aug 17, 2023
@khurrammaqbool khurrammaqbool deleted the feat/add_cadd_container branch August 17, 2023 11:50
@ivadym ivadym linked an issue Aug 22, 2023 that may be closed by this pull request
[User Story] Fix recurrent problems with BALSAMIC containers #1165
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@ivadym ivadym mentioned this pull request Nov 6, 2023
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@ivadym ivadym ivadym approved these changes

@mathiasbio mathiasbio mathiasbio approved these changes

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[User Story] Fix recurrent problems with BALSAMIC containers CADD scores for SNVs and INDELs
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@khurrammaqbool @mathiasbio @ivadym