hotfix(function split)

[karlnyr]

Description

This pull request makes a small fix to the fetch_external method in microSALT/utils/referencer.py. The change corrects a bug where the lower method was missing parentheses, ensuring that species names are properly converted to lowercase before splitting.

Primary function of PR

• Hot-fix
• Patch
• Minor functionality improvement
• New type of analysis
• Backward-breaking functionality improvement
• This change requires internal documents to be updated
• This change requires another repository to be updated

Testing

• bash /home/proj/production/servers/resources/hasta.scilifelab.se/install-microsalt-stage.sh BRANCHNAME
• us
• conda activate S_microSALT
• microSALT analyse --input /path/to/fastq/ SAMPLEINFO_FILE

Test results

These are the results of the tests, and necessary conclusions, that prove the stability of the PR.

Sign-offs

• Approved to run at Clinical-Genomics by @karlnyr or @Clinical-Genomics/micro

[Copilot]

Pull Request Overview

This PR fixes a bug in the fetch_external method where the lower string method was called without parentheses, causing it to reference the method object instead of executing the method to convert the species name to lowercase.

Key Changes

• Added missing parentheses to .lower() method call on line 271 of microSALT/utils/referencer.py

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.