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Changelog

All notable changes to LimsETL will be documented in this file.

Format based on Keep a Changelog.

[v2.1.0] - 2026-02-10

Added

  • argparse-based CLI for getProjectFiles.py with -d flag to derive project number from current working directory

Changed

  • Refactored getProjectFiles.py for PEP 8 compliance
  • Refactored limsETL.py for PEP 8 compliance
  • Switched IRIS_ROOT to test cache location

Docs

  • Rewrote CLAUDE.md with full architecture details

[v2.0.1] - 2025-09-11

Added

  • Environment zone detection utility in limsETL.py with get_zone_from_env() function
  • FASTQ folder root constants for JUNO and IRIS zones
  • Claude Code project documentation (CLAUDE.md)
  • Dynamic zone detection for path replacement
  • Comprehensive README documentation

Changed

  • Enhanced FASTQ path handling with zone-aware path replacement
  • Improved project output formatting to use f-strings
  • Updated IRIS zone detection to use prefix matching instead of exact match
  • Refactored path handling for better IRIS zone compatibility

Fixed

  • IRIS zone detection now handles zone variants robustly using startswith("IRIS")
  • Null value handling in sample metadata parsing for species, baitSet, and investigatorSampleId fields
  • Auto-generation of investigatorSampleId from file path when missing

[2024-01-31]

Changed

  • Added configuration module setup check in limsETL.py

[2024-01-12]

Added

  • Draft pairing manifest file creation in makeVariantProject.R
  • Long format pairing workflow: SampleID,PatientID,Type
  • SSHFuse file ignore pattern (._* files) in .gitignore

Changed

  • Enhanced pairing workflow to support editable manifest files
  • Pipeline pairing file generation from manifest

Fixed

  • Primary IGO ID validation to handle duplicate/redundant IGO IDs
  • Prevention of duplication issues from non-primary IGO IDs (e.g., 12345_B_1_1)
  • Filtering to ensure only primary IGO IDs are processed

[2024-01-12] - Starting Point (8c8116d)

Base merge from development branch including:

  • Project file extraction improvements
  • Variant calling project file generation enhancements
  • Request merging functionality
  • Known targets configuration updates