Merge pull request #1508 from davidecarlson/contaminants_multiqc_fix

Fix missing Bracken results in the MultiQC report

Author: davidecarlson

CHANGELOG.md

@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1490](https://github.com/nf-core/rnaseq/pull/1490) - Make genomic FASTA input optional
 - [PR #1496](https://github.com/nf-core/rnaseq/pull/1496) - Template update for nf-core/tools v3.2.0
 - [PR #1499](https://github.com/nf-core/rnaseq/pull/1499) - Bump MultiQC module to 1.27
+- [PR #1508](https://github.com/nf-core/rnaseq/pull/1508) - Fix missing Bracken results in the MultiQC report
 
 # 3.18.0 - 2024-12-19
 

docs/output.md

@@ -697,7 +697,7 @@ The plot on the left hand side shows the standard PC plot - notice the variable
 
 </details>
 
-[Kraken2](https://ccb.jhu.edu/software/kraken2/) is a taxonomic classification tool that uses k-mer matches paired with a lowest common ancestory (LCA) algorithm to classify species reads. [Bracken](https://ccb.jhu.edu/software/bracken/) is a statistical method to generate abundance estimates based off of the Kraken2 output. These algorithms are run on unaligned sequences to detect potential contamination of samples. MultiQC reports the top 5 taxon members detected at the level of classification used for Bracken, with toggles available for higher taxonomic levels. If Bracken is skipped, MultiQC will report the top 5 species detected by Kraken2.
+[Kraken2](https://ccb.jhu.edu/software/kraken2/) is a taxonomic classification tool that uses k-mer matches paired with a lowest common ancestory (LCA) algorithm to classify species reads. [Bracken](https://ccb.jhu.edu/software/bracken/) is a statistical method to generate abundance estimates based off of the Kraken2 output. These algorithms are run on unaligned sequences to detect potential contamination of samples. MultiQC reports the top 5 taxon members detected at the level of classification used for Bracken, with toggles available for higher taxonomic levels. Because MultiQC no longer has a separate Bracken module, results for Bracken will appear under the Kraken heading in the MultiQC report. If Bracken is skipped, MultiQC will report the top 5 species detected by Kraken2.
 
 ![MultiQC - Bracken top species plot](images/bracken-top-n-plot.png)
 

workflows/rnaseq/assets/multiqc/multiqc_config.yml

@@ -97,7 +97,6 @@ run_modules:
   - rseqc
   - qualimap
   - kraken
-  - bracken
 
 # Order of modules
 
@@ -160,13 +159,9 @@ sp:
     fn: "*.flagstat"
   samtools/idxstats:
     fn: "*.idxstats*"
-
   kraken:
-    fn: "*report.txt"
-
-  bracken:
-    fn: "*.kraken2.report_bracken.txt"
-
+    - fn: "*.kraken2.report.txt"
+    - fn: "*.kraken2.report_bracken.txt"
   rseqc/bam_stat:
     fn: "*.bam_stat.txt"
   rseqc/gene_body_coverage: