Cristina Tuñí i Domínguez

clarification of star and salmon outputs from issue #722

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This PR fixes #722 by adding small clarifications on `salmon` output files. ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ]...

Qualimap assigns more reads to exonic regions than total reads in the sample

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### Description of the bug A while ago we realized that `QUALIMAP` assigns more reads to exonic+intronic+intergenic than total reads in the sample. We subsampled the paired-end SRA FASTQ to...

added patch command for subworkflows

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Related to issue: https://github.com/nf-core/tools/issues/1891 Is there a straightforward way to test this?

kraken2 assigning exactly the same taxonomy at low magnitudes to very different samples

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We've been running kraken2 with our RNA-Seq samples to check for contamination for a year more or less. At first we were surprised to find some contamination that we deemed...

Add HTSEQ/COUNT module

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Documentation on how to add modules https://nf-co.re/docs/tutorials/nf-core_components/adding_modules_to_pipelines

Add the necessary genome/reference "preparation" steps

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### Description of feature Such as star index creation if only fasta and GTF provided, for example

### Description of feature Always cool to have a hex logo for the pipeline to turn into stickers 👀