Merge pull request #369 from nf-core/standardize-conversion-workflow

Standardize conversion workflow

Author: grst

CHANGELOG.md

@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - 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))
 
 ## v2.7.1 - 2024-08-13