leafworker (v0.3.1)

This patch release of leafworker applies an important patch to IsoformSwitchAnalyzeR to prevent incorrect type casting in design matrices, resolving potential rank issues during analysis. It also updates the output directory structure for Salmon count matrices to explicitly include the batch ID. This new option can be supplied to prevent overwriting of jointly-called files across runs of the pipeline.

Bug fixes:

• IsoformSwitchAnalyzeR Patch: Applied a runtime patch to IsoformSwitchAnalyzeR's importRdata function to prevent automatic type casting of numeric/integer columns in the design matrix. This resolves an issue where auto-casting could cause the design matrix to become non-full rank (related to IsoformSwitchAnalyzeR issue #247).
• Salmon Output Path: Updated the output paths for Salmon quantification matrices (raw_counts.tsv and tpm_normalized.tsv) to include the batch_id in the directory structure. This ensures outputs are correctly organized by different runs or downstream analysis batches of the pipeline.

Full Changelog: https://github.com/OpenOmics/leafworker/compare/v0.3.0...v0.3.1