Merge pull request #1395 from nf-core/dev

RC 3.16.0

CHANGELOG.md

@@ -3,11 +3,62 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[3.16.0](https://github.com/nf-core/rnaseq/releases/tag/3.16.0)] - 2024-10-02
+
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Adam Talbot](https://github.com/adamrtalbot)
+- [Ezra Greenberg](https://github.com/egreenberg7)
+- [Jonathan Manning](https://github.com/pinin4fjords)
+- [Matthias Zepper](https://github.com/MatthiasZepper)
+- [Maxime Garcia](https://github.com/maxulysse)
+- [Paolo Di Tommaso](https://github.com/pditommaso)
+- [Phil Ewels](https://github.com/ewels)
+- [Shaun Regenbaum](https://github.com/Shaun-Regenbaum)
+
+### Enhancements & fixes
+
+- [PR #1376](https://github.com/nf-core/rnaseq/pull/1376) - Fix invalid named parameter syntax
+- [PR #1386](https://github.com/nf-core/rnaseq/pull/1386) - Bump pipeline version to 3.16.0dev
+- [PR #1388](https://github.com/nf-core/rnaseq/pull/1388) - Adding Kraken2/Bracken on unaligned reads as an additional quality control step to detect sample contamination
+- [PR #1389](https://github.com/nf-core/rnaseq/pull/1389) - Update animated subway map
+- [PR #1393](https://github.com/nf-core/rnaseq/pull/1393) - Use quay.io for bedtools/genomecov to solve issue with nf-core download
+
+### Parameters
+
+| Old parameter | New parameter               |
+| ------------- | --------------------------- |
+|               | `--contaminant_screening`   |
+|               | `--kraken_db`               |
+|               | `--save_kraken_assignments` |
+|               | `--save_kraken_unassigned`  |
+|               | `--bracken_precision`       |
+
+> **NB:** Parameter has been **updated** if both old and new parameter information is present.
+> **NB:** Parameter has been **added** if just the new parameter information is present.
+> **NB:** Parameter has been **removed** if new parameter information isn't present.
+
+### Software dependencies
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `Kraken2`  | ----------- | 2.1.3       |
+| `Bracken`  | ----------- | 2.9         |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
+
 ## [[3.15.1](https://github.com/nf-core/rnaseq/releases/tag/3.15.1)] - 2024-09-16
 
 ### Enhancements & fixes
 
 - [PR #1374](https://github.com/nf-core/rnaseq/pull/1374) - Bump pipeline version to 3.16.0dev
+- [PR #1379](https://github.com/nf-core/rnaseq/pull/1379) - Enhance pipeline level test snapshots
 - [PR #1380](https://github.com/nf-core/rnaseq/pull/1380) - Fix issues with R modules changing sample names
 - [PR #1381](https://github.com/nf-core/rnaseq/pull/1381) - Update all modules following massive conda usage update in nf-core modules
 - [PR #1382](https://github.com/nf-core/rnaseq/pull/1381) - Slight fixes for rnaseq preprocessing

CITATIONS.md

@@ -16,6 +16,10 @@
 
   > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824.
 
+- [Bracken](https://doi.org/10.7717/peerj-cs.104)
+
+  > Lu, J., Breitwieser, F. P., Thielen, P., & Salzberg, S. L. (2017). Bracken: estimating species abundance in metagenomics data. PeerJ. Computer Science, 3(e104), e104. https://doi.org/10.7717/peerj-cs.104
+
 - [fastp](https://www.ncbi.nlm.nih.gov/pubmed/30423086/)
 
   > Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560. PubMed PMID: 30423086; PubMed Central PMCID: PMC6129281.
@@ -38,6 +42,10 @@
 
   > Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4. Epub 2019 Aug 2. PubMed PMID: 31375807.
 
+- [Kraken2](https://doi.org/10.1186/s13059-019-1891-0)
+
+  > Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257. https://doi.org/10.1186/s13059-019-1891-0
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

README.md

@@ -46,6 +46,7 @@
     3. [`dupRadar`](https://bioconductor.org/packages/release/bioc/html/dupRadar.html)
     4. [`Preseq`](http://smithlabresearch.org/software/preseq/)
     5. [`DESeq2`](https://bioconductor.org/packages/release/bioc/html/DESeq2.html)
+    6. [`Kraken2`](https://ccb.jhu.edu/software/kraken2/) -> [`Bracken`](https://ccb.jhu.edu/software/bracken/) on unaligned sequences; _optional_
 15. Pseudoalignment and quantification ([`Salmon`](https://combine-lab.github.io/salmon/) or ['Kallisto'](https://pachterlab.github.io/kallisto/); _optional_)
 16. Present QC for raw read, alignment, gene biotype, sample similarity, and strand-specificity checks ([`MultiQC`](http://multiqc.info/), [`R`](https://www.r-project.org/))