bump version and update changelog

CHANGELOG.md

@@ -3,13 +3,25 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## v3.0.0 - 2024-12-09
 
-- Remove universc workflow from pipeline ([#289](https://github.com/nf-core/scrnaseq/issues/289))
-- Add `--save_align_intermeds` parameter that publishes BAM files to the output directory (for `starsolo`, `cellranger` and `cellranger multi`) ([#384](https://github.com/nf-core/scrnaseq/issues/384))
-- Added support for pre-built indexes in `genomes.config` file for `cellranger`, `cellranger-arc`, `simpleaf` and `simpleaf txp2gene` ([#371](https://github.com/nf-core/scrnaseq/issues/371))
-- Cleanup and fix bugs in matrix conversion code, and change to use anndataR for conversions, and cellbender for emptydrops call. ([#369](https://github.com/nf-core/scrnaseq/pull/369))
-- Fix problem with `test_full` that was not running out of the box, since code was trying to overwrite parameters in the workflow, which is not possible ([#366](https://github.com/nf-core/scrnaseq/issues/366))
+## Backwards-incompatible changes
+
+- Remove universc workflow from pipeline ([#289](https://github.com/nf-core/scrnaseq/issues/289)).
+- Remove emptydrops from the pipeline, in favor of cellbender ([#369](https://github.com/nf-core/scrnaseq/pull/369)).
+
+## Additions
+
+- Add `--save_align_intermeds` parameter that publishes BAM files to the output directory (for `starsolo`, `cellranger` and `cellranger multi`) ([#384](https://github.com/nf-core/scrnaseq/issues/384)).
+
+## Fixes
+
+- Add support for pre-built indexes in `genomes.config` file for `cellranger`, `cellranger-arc`, `simpleaf` and `simpleaf txp2gene` ([#371](https://github.com/nf-core/scrnaseq/issues/371)).
+- Refactor matrix conversion code. Output from all aligners is initially converted to AnnData h5ad that is used for
+  downstream code such as cellbender. H5ad objects are converted to Seurat and SingleCellExperiment at the end
+  using anndataR. This reduced the pipeline complexity and resolved various issues relating to output format conversion
+  ([#369](https://github.com/nf-core/scrnaseq/pull/369)).
+- Fix problem with `test_full` that was not running out of the box, since code was trying to overwrite parameters in the workflow, which is not possible ([#366](https://github.com/nf-core/scrnaseq/issues/366)).
 
 ## v2.7.1 - 2024-08-13
 

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/scrnaseq/tree/dev" target="_blank">nf-core/scrnaseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/scrnaseq/releases/tag/3.0.0" target="_blank">nf-core/scrnaseq</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/scrnaseq/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/scrnaseq/3.0.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-scrnaseq-methods-description":
     order: -1000

nextflow.config

@@ -290,7 +290,7 @@ manifest {
     description     = """Pipeline for processing 10x Genomics single cell rnaseq data"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = '2.8.0dev'
+    version         = '3.0.0'
     doi             = '10.5281/zenodo.3568187'
 }