search

nf-core / rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
https://nf-co.re/rnaseq
MIT License
824 stars 681 forks source link

Show Salmon-based strand inference in MultiQC report #1318

Closed pinin4fjords closed 1 month ago

pinin4fjords commented 1 month ago

Description of feature

Confusion frequently arises around the auto strandedness detection from Salmon and how it matches (or rather does not) with that from RSeQC towards the end of the pipeline. It would help if we could at least show the Salmon-detected strandedness in the MultiQC report.

This requires:

  1. MultiQC to detect and report strandedness from Salmon
  2. The pipeline to be rewired to pass the Salmon JSON files from the subsampling/ Salmon workflow (not the main Salmon process used for quantification) to MultiQC show the results and distinguish them from the Salmon results from quantification.

1) should have been done, already, but there was a bug in MultiQC (now fixed), and we'll need a new release for that to be resolved fully.

I suspect 2) is going to be fiddly.

pinin4fjords commented 1 month ago

Solved in https://github.com/nf-core/rnaseq/pull/1306