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Update command syntax to include config option in microsalt execution - #5069

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add-microsalt-config-to-call
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Update command syntax to include config option in microsalt execution#5069
diitaz93 wants to merge 7 commits into
masterfrom
add-microsalt-config-to-call

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@diitaz93

@diitaz93 diitaz93 commented May 4, 2026 •
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Description

Fix the call to the microSALT binary to put the config file in the correct order

PR in servers: https://github.com/Clinical-Genomics/servers/pull/1821

Added

  • Support for parsing the microsalt config file from cg.yaml
  • MicrosaltCaseConfig now saves the pipeline config as an attribute

Changed

  • The get_start_command in cg.services.analysis_starter.configurator.models.microsalt.MicrosaltCaseConfig adds the pipeline config after calling the pipeline binary
  • Use the pipeöine config in the command to get the microsalt version

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 add-microsalt-config-to-call -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 requested a review from a team as a code owner May 4, 2026 14:37
@diitaz93 diitaz93 linked an issue May 4, 2026 that may be closed by this pull request
Make microSALT start with --config and path to the config #5045
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karlnyr
karlnyr requested changes May 5, 2026
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Comment thread cg/services/analysis_starter/configurator/models/microsalt.py Outdated
Comment thread tests/services/analysis_starter/test_case_configs.py Outdated
@diitaz93
diitaz93 requested a review from karlnyr May 5, 2026 14:41
karlnyr
karlnyr reviewed May 7, 2026
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@karlnyr karlnyr left a comment

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Works and looks like a charm!

@sonarqubecloud

sonarqubecloud Bot commented May 26, 2026

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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 SonarQube Cloud

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@karlnyr karlnyr karlnyr approved these changes

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Make microSALT start with --config and path to the config

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@diitaz93 @karlnyr