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Remove old code from starting analyses pt 2#4809

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diitaz93 merged 17 commits intomasterfrom
clean-starting-analysis2
Jan 27, 2026
Merged

Remove old code from starting analyses pt 2#4809
diitaz93 merged 17 commits intomasterfrom
clean-starting-analysis2

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@diitaz93 diitaz93 commented Jan 8, 2026

Description

Changed

  • Removed link and resolve_compression from the list of commands of MIP-DNA
  • Removed unused Nextflow constants
  • Remove compute_env_base and nextflow_binary_path attributes of the NFAnalysisAPIs
  • Remove unused methods from NfAnalysisAPI
  • Remove compute_env from NF config classes in cg_config

Fixed

  • Fixed vulture whiteliest

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 ...

@diitaz93 diitaz93 changed the title Clean starting analysis2 Remove old code from starting analyses pt 2 Jan 8, 2026
@diitaz93 diitaz93 marked this pull request as ready for review January 8, 2026 16:02
@diitaz93 diitaz93 requested a review from a team as a code owner January 8, 2026 16:02
@diitaz93 diitaz93 requested a review from islean January 20, 2026 07:43
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Super! 💯

@sonarqubecloud
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@diitaz93 diitaz93 merged commit 5700e43 into master Jan 27, 2026
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@diitaz93 diitaz93 deleted the clean-starting-analysis2 branch January 27, 2026 08:13
@diitaz93
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Deployed to hasta stage and prod

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2 participants