From d7a0e96a446ba57a7c5a6aa0f74c32bd924a9331 Mon Sep 17 00:00:00 2001 From: Harrison Pirt Date: Thu, 28 May 2026 10:54:49 +0000 Subject: [PATCH] wf-transcriptomes 2.0.0-rc1 --- CHANGELOG.md | 42 +++++++++++++++++++++++++----------- README.md | 2 +- docs/01_brief_description.md | 2 +- nextflow.config | 4 ++-- nextflow_schema.json | 2 +- 5 files changed, 34 insertions(+), 18 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d160211..1b4e2a0 100644 --- a/CHANGELOG.md +++ b/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: - - Pipeline overview now appears before pipeline parameters in README. - - Fastcat FASTQ pre-processing program has been updated to 0.24.2, it is more robust to malformed FASTQ input. - -### Added -- Updated to wf-template v6.0.0, adding: - - Support for workflows to define non-main entrypoints for additional functionality. - - ezcharts 0.16.1, to provide UpSetPlot, BaseComposition and polya components - -### Fixed -- Updated to wf-template v6.0.0, fixing: - - `configure_igv` process crashes when reference names include special characters. +- Replaced the previous `StringTie/GffCompare/Salmon-based` transcript discovery and quantification workflow with a `bambu`-based workflow. +- The main transcriptome result is now a shared cohort transcriptome built from all samples together. +- 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`. +- Differential transcript usage continues to use `DEXSeq`, now driven from the shared bambu outputs. +- Transcript classification and QC is now performed for both cohort and per-sample transcriptomes with `SQANTI3`. +- Workflow prerequisites and experimental design inputs are validated earlier to catch common setup issues sooner. +- Output structure has been reorganised around: + - `cohort/` + - `samples//` + - `de_analysis//` +- Differential analysis outputs are now grouped per contrast under `de_analysis//`. +- 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. diff --git a/README.md b/README.md index eea3c1c..c16605a 100644 --- a/README.md +++ b/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. diff --git a/docs/01_brief_description.md b/docs/01_brief_description.md index ed4bddb..537354e 100644 --- a/docs/01_brief_description.md +++ b/docs/01_brief_description.md @@ -1 +1 @@ -Long-read transcriptome analysis using bambu with optional SQANTI3 QC, DESeq2, and DEXSeq. \ No newline at end of file +Long-read transcript discovery, quantification, differential expression, QC and mod counting. \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 4b12865..a1cdbb8 100644 --- a/nextflow.config +++ b/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 { diff --git a/nextflow_schema.json b/nextflow_schema.json index e7fddfd..1bb5adf 100644 --- a/nextflow_schema.json +++ b/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": {