[3.8] - 2022-05-25
⚠️ Major enhancements
Fixed a well hidden bug in the UMI processing mode of the pipeline when using --with_umi --aligner star_salmon as reported by Lars Roed Ingerslev. Paired-end BAM files were not appropriately name sorted after umi_tools dedup which ultimately resulted in incorrect reading and quantification with Salmon. If you have used previous versions of the pipeline to analyse paired-end UMI data it will need to be reprocessed using this version of the pipeline. See #828 for more context.
Enhancements & fixes
- [#824] - Add explicit docs for usage of featureCounts in the pipeline
- [#825] - Pipeline fails due to trimming related removal of all reads from a sample
- [#827] - Control generation of --output-stats when running umi-tools dedup
- [#828] - Filter BAM output of UMI-tools dedup before passing to Salmon quant
- Updated pipeline template to nf-core/tools 2.4.1
Parameters
| Old parameter | New parameter |
|---|---|
--min_trimmed_reads
| |
--umitools_dedup_stats
|