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feat: add htslib container #1234

Merged
merged 5 commits into from
Aug 22, 2023
Merged

feat: add htslib container #1234

merged 5 commits into from
Aug 22, 2023

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khurrammaqbool
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@khurrammaqbool khurrammaqbool commented Aug 21, 2023 •
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This PR:

Added: htslib container with samtools, bcftools, tabix and bgzip.

Review and tests:

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

@khurrammaqbool khurrammaqbool self-assigned this Aug 21, 2023
@khurrammaqbool khurrammaqbool requested a review from a team as a code owner August 21, 2023 09:30
@khurrammaqbool khurrammaqbool mentioned this pull request Aug 21, 2023
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codecov bot commented Aug 21, 2023 •
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Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (4e613c8) 99.42% compared to head (9057456) 99.42%.

Additional details and impacted files 
@@           Coverage Diff            @@
##           develop    #1234   +/-   ##
========================================
  Coverage    99.42%   99.42%           
========================================
  Files           41       41           
  Lines         1918     1919    +1     
========================================
+ Hits          1907     1908    +1     
  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/constants/cache.py 100.00% <100.00%> (ø)

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ivadym
ivadym approved these changes Aug 21, 2023
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Looks good! 👍

Left you some minor comments 😊

docs/programming_guide.rst Outdated Show resolved Hide resolved
BALSAMIC/containers/htslib/Dockerfile Outdated Show resolved Hide resolved
BALSAMIC/containers/htslib/Dockerfile Outdated Show resolved Hide resolved
BALSAMIC/containers/htslib/Dockerfile Outdated Show resolved Hide resolved
@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

@khurrammaqbool khurrammaqbool merged commit eb21495 into develop Aug 22, 2023
@khurrammaqbool khurrammaqbool deleted the feat/add_htslib_container branch August 22, 2023 09:01
@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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6 tasks
@khurrammaqbool khurrammaqbool linked an issue Oct 5, 2023 that may be closed by this pull request
CN-LoH analysis #1105
Closed
@ivadym ivadym mentioned this pull request Nov 6, 2023
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@khurrammaqbool khurrammaqbool mentioned this pull request Nov 13, 2023
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@ivadym ivadym ivadym approved these changes

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Successfully merging this pull request may close these issues.

[User Story] Fix recurrent problems with BALSAMIC containers CN-LoH analysis
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@khurrammaqbool @ivadym