Merge branch 'v2releasechanglog' into 'dev'

wf-transcriptomes 2.0.0-rc1

See merge request epi2melabs/workflows/wf-transcriptomes!315

CHANGELOG.md

@@ -4,21 +4,37 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## [v2.0.0-rc1]
+
+This release refreshes `wf-transcriptomes` around a new reference-guided transcriptomics workflow built on `bambu`, with `SQANTI3` transcript classification and QC, `DESeq2` for differential gene expression, `DEXSeq` for differential transcript usage, and per-sample modified base summarisation with `modkit` when modification tags are present in aligned BAMs.
 
 ### Changed
-- Updated to wf-template v6.0.0 to maintain compliance with our latest wf-template standard, changing:
+- Replaced the previous `StringTie/GffCompare/Salmon-based` transcript discovery and quantification workflow with a `bambu`-based workflow.
-  - Pipeline overview now appears before pipeline parameters in README.
+- The main transcriptome result is now a shared cohort transcriptome built from all samples together.
-  - Fastcat FASTQ pre-processing program has been updated to 0.24.2, it is more robust to malformed FASTQ input.
+- Per-sample transcriptome FASTA outputs are now supplemented with per-sample GTF files, count tables, transcript metadata and QC summaries.
-
+- Differential gene expression now uses `DESeq2`.
-### Added
+- Differential transcript usage continues to use `DEXSeq`, now driven from the shared bambu outputs.
-- Updated to wf-template v6.0.0, adding:
+- Transcript classification and QC is now performed for both cohort and per-sample transcriptomes with `SQANTI3`.
-    - Support for workflows to define non-main entrypoints for additional functionality.
+- Workflow prerequisites and experimental design inputs are validated earlier to catch common setup issues sooner.
-    - ezcharts 0.16.1, to provide UpSetPlot, BaseComposition and polya components
+- Output structure has been reorganised around:
-
+  - `cohort/`
-### Fixed
+  - `samples/<alias>/`
-- Updated to wf-template v6.0.0, fixing:
+  - `de_analysis/<contrast>/`
-    - `configure_igv` process crashes when reference names include special characters.
+- Differential analysis outputs are now grouped per contrast under `de_analysis/<contrast>/`.
+- The workflow now supports two bambu modes via `--transcriptome_mode`:
+  - `discover`
+  - `fixed_annotation`
+- Per-sample modified base summarisation from aligned BAMs containing `MM` and `ML` tags using modkit, including:
+  - `bedMethyl` pileup
+  - per-sample modification summary tables
+  - per-modification bigWig tracks
+- Reports have been refreshed with new components including:
+    - Sample-level hierarchical clustering, PCA and distance heatmap plots
+    - Contrast-level interactive volcano plots
+### Removed
+- `--transcriptome_source` parameter; use `--transcriptome_mode` instead.
+- `--ref_transcriptome` parameter; use `--transcriptome_mode fixed_annotation` together with `--ref_genome` and `--ref_annotation`.
+- Dependence on the older `StringTie/GffCompare/Salmon` transcriptomics pathway.
 
 ## [v1.7.2]
 This patch release of wf-transcriptomes updates internal workflow naming, and does not affect any workflow outputs.

README.md

@@ -1,6 +1,6 @@
 # Transcriptomes
 
-Long-read transcriptome analysis using bambu with optional SQANTI3 QC, DESeq2, and DEXSeq.
+Long-read transcript discovery, quantification, differential expression, QC and mod counting.
 
 
 

docs/01_brief_description.md

@@ -1 +1 @@
-Long-read transcriptome analysis using bambu with optional SQANTI3 QC, DESeq2, and DEXSeq.
+Long-read transcript discovery, quantification, differential expression, QC and mod counting.

nextflow.config

@@ -65,10 +65,10 @@ manifest {
     name            = 'epi2me-labs/wf-transcriptomes'
     author          = 'Oxford Nanopore Technologies'
     homePage        = 'https://github.com/epi2me-labs/wf-transcriptomes'
-    description     = 'Long-read transcriptome analysis using bambu with optional SQANTI3 QC, DESeq2, and DEXSeq.'
+    description     = 'Long-read transcript discovery, quantification, differential expression, QC and mod counting.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = 'v0.1.0'
+    version         = 'v2.0.0-rc1'
 }
 
 process {

nextflow_schema.json

@@ -3,7 +3,7 @@
   "$id": "https://raw.githubusercontent.com/epi2me-labs/wf-transcriptomes/master/nextflow_schema.json",
   "title": "epi2me-labs/wf-transcriptomes",
   "workflow_title": "Transcriptomes",
-  "description": "Long-read transcriptome analysis using bambu with optional SQANTI3 QC, DESeq2, and DEXSeq.",
+  "description": "Long-read transcript discovery, quantification, differential expression, QC and mod counting.",
   "url": "https://github.com/epi2me-labs/wf-transcriptomes",
   "type": "object",
   "definitions": {