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Clean up run_analysis method for nf_analysis #2772

Merged
merged 9 commits into from
Dec 14, 2023
Merged

Clean up run_analysis method for nf_analysis #2772

merged 9 commits into from
Dec 14, 2023

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fevac
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@fevac fevac commented Dec 14, 2023 •
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Description

Changed

  • Split run_analysis method

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

  • cg workflow rnafusion run -d CASE
  • cg workflow rnafusion run -d --use-nextflow CASE
  • cg workflow rnafusion run -d --from-start CASE

Expected test outcome

  • run command shows correctly

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 ...

@fevac fevac marked this pull request as ready for review December 14, 2023 15:11
@fevac fevac requested a review from a team as a code owner December 14, 2023 15:11
henrikstranneheim
henrikstranneheim approved these changes Dec 14, 2023
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@henrikstranneheim henrikstranneheim left a comment

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Nice 👍

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fevac and others added 4 commits December 14, 2023 16:32
@sonarqubecloud SonarQubeCloud
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Quality Gate Passed Quality Gate passed

Kudos, no new issues were introduced!

0 New issues
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

@sonarqubecloud SonarQubeCloud
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Quality Gate Passed Quality Gate passed

Kudos, no new issues were introduced!

0 New issues
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

@fevac
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fevac commented Dec 14, 2023

tests are passing

@fevac fevac merged commit 0afaf6f into master Dec 14, 2023
8 checks passed
@fevac fevac deleted the refactor_nf branch December 14, 2023 15:53
@fevac
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fevac commented Dec 14, 2023

  • deploy to stage
image
  • deployed to prod
image

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Reviewers

@seallard seallard seallard approved these changes

@henrikstranneheim henrikstranneheim henrikstranneheim approved these changes

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3 participants
@fevac @henrikstranneheim @seallard