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Update balsamic tags & upload a CGH file to Scout #1477

Merged
merged 25 commits into from
May 19, 2022
Merged

Update balsamic tags & upload a CGH file to Scout #1477

merged 25 commits into from
May 19, 2022

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ivadym
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@ivadym ivadym commented May 4, 2022 •
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Description

Added

  • balsamic-umi delivery option
  • vcf2cytosure upload to Scout
  • --pon-cnn config case flag for BALSAMIC
  • --genome-version config case flag for BALSAMIC

Changed

  • Balsamic delivery tags

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-cg-stage.sh [THIS-BRANCH-NAME]

How to test

  • do ...

Expected test outcome

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

Review

  • code approved by
  • 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 ...

ivadym added 12 commits May 3, 2022 15:26
@ivadym ivadym mentioned this pull request May 9, 2022
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@ivadym
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ivadym commented May 10, 2022

Tests

Updated command line

Screen Shot 2022-05-10 at 13 09 13

Balsamic delivery to customer inbox

cg deliver analysis -d balsamic-umi -c ...

Screen Shot 2022-05-10 at 13 27 30

Upload to scout of a CGH file

Screen Shot 2022-05-10 at 13 35 17

Screen Shot 2022-05-10 at 13 36 40

henrikstranneheim
henrikstranneheim reviewed May 10, 2022
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Looks great so far! Well done

cg/cli/workflow/balsamic/options.py Outdated Show resolved Hide resolved
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cg/cli/workflow/balsamic/options.py Outdated Show resolved Hide resolved
cg/meta/upload/scout/balsamic_config_builder.py Outdated Show resolved Hide resolved
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@ivadym ivadym marked this pull request as ready for review May 10, 2022 16:05
patrikgrenfeldt
patrikgrenfeldt approved these changes May 18, 2022
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👍

cg/constants/constants.py 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

@ivadym ivadym merged commit 276f318 into master May 19, 2022
@ivadym ivadym deleted the update/balsamic_tags branch May 19, 2022 12:04
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ivadym commented May 19, 2022

Deployed:

Screen Shot 2022-05-19 at 14 10 57

@ivadym ivadym mentioned this pull request May 19, 2022
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@ivadym ivadym mentioned this pull request Jun 13, 2022
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Reviewers

@henrikstranneheim henrikstranneheim henrikstranneheim left review comments

@patrikgrenfeldt patrikgrenfeldt patrikgrenfeldt approved these changes

@barrystokman barrystokman Awaiting requested review from barrystokman

@Mropat Mropat Awaiting requested review from Mropat

@henningonsbring henningonsbring Awaiting requested review from henningonsbring

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3 participants
@ivadym @henrikstranneheim @patrikgrenfeldt