From a5d683ded42ca82eeffe7de32c8f56081924daaa Mon Sep 17 00:00:00 2001 From: davidecarlson Date: Fri, 28 Feb 2025 10:08:28 -0500 Subject: [PATCH 1/4] add Kraken2 multiqc fixes suggested by Ezra Greenberg to --- workflows/rnaseq/assets/multiqc/multiqc_config.yml | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml index 4af07dc67..1732e4116 100644 --- a/workflows/rnaseq/assets/multiqc/multiqc_config.yml +++ b/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: "*report.txt" + - fn: "*.kraken2.report_bracken.txt" rseqc/bam_stat: fn: "*.bam_stat.txt" rseqc/gene_body_coverage: From 0c8def9ef3923985ce2863aad259ae123c43be9b Mon Sep 17 00:00:00 2001 From: davidecarlson Date: Mon, 3 Mar 2025 14:43:11 -0500 Subject: [PATCH 2/4] added clarification regarding Bracken output in the MultiQC report to the output.md docs --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index 34326ea23..8c0457f77 100644 --- a/docs/output.md +++ b/docs/output.md @@ -697,7 +697,7 @@ The plot on the left hand side shows the standard PC plot - notice the variable -[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) From 149619b985a4871cb2822cce0dabef3f29bb992a Mon Sep 17 00:00:00 2001 From: davidecarlson Date: Mon, 3 Mar 2025 14:55:16 -0500 Subject: [PATCH 3/4] updated changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4776111d8..9e4dde0e3 100644 --- a/CHANGELOG.md +++ b/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 From 27fe7631d5b11a7a454cb975d01f4b969de63178 Mon Sep 17 00:00:00 2001 From: davidecarlson Date: Fri, 7 Mar 2025 08:55:14 -0500 Subject: [PATCH 4/4] make multqic function looking for kraken2 report more specific --- workflows/rnaseq/assets/multiqc/multiqc_config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml index ea760395b..9a98b1705 100644 --- a/workflows/rnaseq/assets/multiqc/multiqc_config.yml +++ b/workflows/rnaseq/assets/multiqc/multiqc_config.yml @@ -160,7 +160,7 @@ sp: samtools/idxstats: fn: "*.idxstats*" kraken: - - fn: "*report.txt" + - fn: "*.kraken2.report.txt" - fn: "*.kraken2.report_bracken.txt" rseqc/bam_stat: fn: "*.bam_stat.txt"