v1.6.1

1.6.1 (2026-07-26)

Documentation

• regenerate snakevision rule graph for the transcript stage (f0a8e75)
• regenerate snakevision rule graph for the transcript stage (eb1d13b)

v1.6.0

1.6.0 (2026-07-26)

Added

• dte: add DTU interpretation layer + annotated report (T4/T8) (9659a03)
• transcript-level DTE via edgeR catchSalmon (dte_all) (76f2032)

Fixed

• dte: add readr + jsonlite to r-transcript env (catchSalmon deps) (2bee4e2)

v1.5.0

1.5.0 (2026-07-26)

Added

• add transcript-level differential expression from Salmon (det_all) (1a8be63)
• transcript-level differential expression from Salmon (det_all) (8ac7586)

v1.4.2

1.4.2 (2026-07-24)

Documentation

• add snakevision rule-graph (tube map) for the current workflow (17dfd79)
• add snakevision rule-graph (tube map) for the current workflow (30280ce)
• fix Docker Hub repo name + drop conceptual diagram from README (803b64f)
• note the one-off snakevision install in the rule-graph regen snippet (53074d1)
• point Docker Hub refs at the real rnaseq-pipeline repo; drop diagram.png (8f0bb65)

v1.4.1

1.4.1 (2026-07-24)

Fixed

• make the Apptainer build work rootless (no /etc/subuid) (d6ae52e)
• mirror the rootless-apt sandbox fix into the Dockerfile (e6e10ed)

v1.4.0

1.4.0 (2026-07-23)

Added

• add opt-in DESeq2 differential-expression + GO/KEGG enrichment stage (2e0ce38)
• add opt-in DESeq2 differential-expression + GO/KEGG enrichment stage (9ffe263)

v1.3.0

1.3.0 (2026-07-23)

Added

• build the RSeQC gene-model BED from the GTF on demand (c638e6f)
• GENCODE v36 reference support + on-demand RSeQC BED generation (4eeaf38)

Fixed

• point config at the GENCODE v36 GTF shipped in ref/ (8da675d)

Documentation

• switch reference download links to GENCODE v36 to match the shipped GTF (db92dd6)

v1.2.1

1.2.1 (2026-07-23)

Documentation

• add Zenodo DOI badge and CITATION.cff identifier (a37b981)
• note the align_chroms/keep_chroms chromosome filters in Configuration (1860cc7)

v1.2.0

1.2.0 (2026-07-23)

Added

• add chromosome-selection filters for alignment (a618af9)
• add chromosome-selection filters for alignment (fac6c56)

v1.1.1

1.1.1 (2026-07-23)

Documentation

• align README with the ATAC-seq template; tidy changelog, badges, and images (e58f762)
• apply the ATAC-seq-style README rewrite (ea8f718)
• move diagram.png into images/ and drop rulegraph.svg (00819bb)
• remove duplicate pipeline figure from README (ddcb985)
• rewrite README in the ATAC-seq template style; drop redundant guides (aa8c95e)
• tidy changelog and refresh README badges (a30f19c)