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fix: cram file hk tags #1307

Merged
merged 4 commits into from
Nov 1, 2023
Merged

fix: cram file hk tags #1307

merged 4 commits into from
Nov 1, 2023

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mathiasbio
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@mathiasbio mathiasbio commented Oct 31, 2023 •
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This PR:

Rename final cram files to remove the final_bam_suffix which should return the tags for the hk file to the original state.

Removed: final_bam_suffix wildcard from cram rules. Final cram names are now in pattern:

  • tumor.[accid].cram
  • normal.[accid].cram

PR specific tests:

  • TGA TN case runs without error
  • And cram files can be stored in HK
image
  • WGS TN case runs without error
  • And cram files can be stored in HK
image

Review and tests:

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

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codecov bot commented Oct 31, 2023 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Files Coverage Δ
BALSAMIC/commands/base.py 100.00% <100.00%> (ø)
BALSAMIC/commands/config/base.py 100.00% <100.00%> (ø)
BALSAMIC/commands/config/case.py 100.00% <100.00%> (+3.44%) ⬆️
BALSAMIC/commands/config/pon.py 100.00% <100.00%> (+4.87%) ⬆️
BALSAMIC/commands/init/base.py 100.00% <100.00%> (ø)
BALSAMIC/commands/options.py 100.00% <100.00%> (ø)
BALSAMIC/commands/report/base.py 100.00% <100.00%> (ø)
BALSAMIC/commands/report/deliver.py 100.00% <100.00%> (ø)
BALSAMIC/commands/report/status.py 100.00% <100.00%> (ø)
BALSAMIC/commands/run/analysis.py 100.00% <100.00%> (ø)
... and 20 more

📢 Thoughts on this report? Let us know!.

@ivadym ivadym changed the base branch from master to develop October 31, 2023 16:06
@mathiasbio mathiasbio self-assigned this Nov 1, 2023
@mathiasbio mathiasbio modified the milestones: Release 14, Release 13 Nov 1, 2023
@mathiasbio mathiasbio marked this pull request as ready for review November 1, 2023 10:26
@mathiasbio mathiasbio requested a review from a team as a code owner November 1, 2023 10:26
@mathiasbio mathiasbio requested a review from ivadym November 1, 2023 10:29
@sonarqubecloud SonarQubeCloud
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sonarqubecloud bot commented Nov 1, 2023

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
No Duplication information No Duplication information

@ivadym ivadym linked an issue Nov 1, 2023 that may be closed by this pull request
Develop Branch: Unable to Store Cases #1285
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@ivadym ivadym mentioned this pull request Nov 1, 2023
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ivadym
ivadym approved these changes Nov 1, 2023
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Clean fix, nice! 🧼 ⭐

@mathiasbio mathiasbio merged commit 3194eaa into develop Nov 1, 2023
@mathiasbio mathiasbio deleted the fix_cram_file_hk_tags branch November 1, 2023 12:43
@ivadym ivadym mentioned this pull request Nov 6, 2023
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@ivadym ivadym ivadym approved these changes

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BALSAMIC
Status: Archived
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Release 13
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Successfully merging this pull request may close these issues.

Develop Branch: Unable to Store Cases
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@mathiasbio @ivadym