BulkSeq Studio 0.14.1

BulkSeq Studio 0.14.1

Maintenance release: removes dead configuration scaffolding so the config no longer advertises behavior the pipeline does not perform. No change to results or to any working configuration.

Changed

• Removed unused config fields that no workflow rule or app code read: workflow.repair_pairs (BBMap repair, never implemented), workflow.differential_expression (the edgeR / limma-voom values were never wired — DESeq2 is selected by input mode), sortmerna.enabled (rRNA filtering is gated on workflow.rrna_filtering), and the STAR overrides outSAMtype / quantMode / sjdb_overhang / genomeSAindexNbases (the indexing rule computes these itself). Existing project configs that still contain these keys load unchanged — the stale keys are ignored.
• Removed the orphaned STAR block in tool_defaults.yaml and a progress-label entry for a "repair" rule that does not exist; updated the README so the feature list shows SortMeRNA rRNA filtering as implemented.

Downloads

Windows:

• BulkSeqStudio-Setup-0.14.1.exe — installer
• BulkSeqStudio-Portable-0.14.1.zip — unzip and run BulkSeqStudio.exe, no install

Linux (x86-64, glibc 2.39+):

• BulkSeqStudio-0.14.1-x86_64.AppImage — mark executable and run
• BulkSeqStudio-linux-0.14.1.tar.gz — extract and run BulkSeqStudio