Skip to content

nf-core/rnaseq v3.8 - Magnesium Mongoose
Compare
Choose a tag to compare
@drpatelh drpatelh released this 25 May 09:45
· 748 commits to master since this release
3.8
6995330
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

[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
Assets 2