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Add q30 check when calculating sample reads #3680

Merged
merged 3 commits into from
Sep 3, 2024
Merged

Add q30 check when calculating sample reads #3680

merged 3 commits into from
Sep 3, 2024

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beatrizsavinhas
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@beatrizsavinhas beatrizsavinhas commented Sep 3, 2024 •
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Description

Closes #3679

Added

  • Check for q30 when calculating Sample.reads
  • Tests for when the q30 of a lane is below the threshold for the sequencer type

How to prepare for test

  • Ssh to relevant server (depending on type of change)
  • Use stage: us
  • Paxa the environment: paxa
  • Install on stage (example for Hasta): 
    bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_cg -t cg -b [THIS-BRANCH-NAME] -a

How to test

  • Do ...

Expected test outcome

  • Check that ...
  • Take a screenshot and attach or copy/paste the output.

Review

  • Tests executed by
  • "Merge and deploy" approved by
    Thanks for filling in who performed the code review and the test!

This version is a

  • MAJOR - when you make incompatible API changes
  • MINOR - when you add functionality in a backwards compatible manner
  • PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

  • Document in ...
  • Deploy this branch on ...
  • Inform to ...

@beatrizsavinhas beatrizsavinhas requested a review from a team as a code owner September 3, 2024 12:50
@beatrizsavinhas beatrizsavinhas changed the title Add reads q30 check and tests. Add reads q30 check Sep 3, 2024
@beatrizsavinhas beatrizsavinhas changed the title Add reads q30 check Add q30 check when calculating sample reads Sep 3, 2024
ChrOertlin
ChrOertlin approved these changes Sep 3, 2024
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@ChrOertlin ChrOertlin left a comment

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Looks good

@beatrizsavinhas beatrizsavinhas mentioned this pull request Sep 3, 2024
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@sonarqubecloud SonarQubeCloud
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sonarqubecloud bot commented Sep 3, 2024

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

@beatrizsavinhas beatrizsavinhas merged commit a826107 into master Sep 3, 2024
9 checks passed
@beatrizsavinhas beatrizsavinhas deleted the 3679-update-sample-reads branch September 3, 2024 13:22
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@ChrOertlin ChrOertlin ChrOertlin approved these changes

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Successfully merging this pull request may close these issues.

Calculation for sample reads does not account for low q30 score
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@beatrizsavinhas @ChrOertlin