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Nallo: add sambamba depth output as deliverable#4843

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peterpru wants to merge 4 commits intomasterfrom
nallo-add-sambamba-housekeeper
Open

Nallo: add sambamba depth output as deliverable#4843
peterpru wants to merge 4 commits intomasterfrom
nallo-add-sambamba-housekeeper

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@peterpru peterpru commented Jan 20, 2026

Description

This PR adds the sambamba output file to the deliverables of Nallo. To be tested in conjuction with the Hermes PR

To the reviewer: will not be merged before testing.

Added

  • sambamba output file to the deliverables of nallo

Changed

Fixed

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 ...

@peterpru peterpru self-assigned this Jan 20, 2026
@peterpru peterpru requested a review from a team as a code owner January 20, 2026 12:48
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peterpru commented Feb 5, 2026

Tests successful, see the corresponding hermes PR: Clinical-Genomics/hermes#156

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sonarqubecloud bot commented Feb 9, 2026

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