nf-core · sofstam · Apr 24, 2025 · Apr 17, 2025 · Apr 17, 2025 · Apr 24, 2025
@@ -7,9 +7,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#600](https://github.com/nf-core/taxprofiler/pull/600) Added metaphlan to multiqc report (❤️ to @harper357 for reporting and added by @sofstam)
+
 ### `Fixed`
 
-- [592](https://github.com/nf-core/taxprofiler/pull/592) improved json schema (by @microlei)
+- [#592](https://github.com/nf-core/taxprofiler/pull/592) improved json schema (by @microlei)
 
 ### `Dependencies`
 

@@ -44,14 +44,16 @@ report_section_order:
     order: 80
   centrifuge:
     order: 70
-  malt:
+  metaphlan:
     order: 60
-  diamond:
+  malt:
     order: 50
-  kaiju:
+  diamond:
     order: 40
-  motus:
+  kaiju:
     order: 30
+  motus:
+    order: 20
 
 export_plots: true
 
@@ -77,6 +79,7 @@ run_modules:
   - diamond
   - malt
   - motus
+  - metaphlan
   - custom_content
 
 sp:
@@ -284,7 +287,10 @@ table_columns_placement:
     "Number of ref-mOTUs": 1860
     "Number of meta-mOTUs": 1870
     "Number of ext-mOTUs": 1880
-
+  metaphlan:
+    tax_rank: 1900
+    taxonomy: 1910
+    rel_abundance: 1920
 table_columns_visible:
   FastQC / Falco (pre-Trimming):
     total_sequences: true
@@ -362,6 +368,7 @@ table_columns_visible:
   Kaiju: false
   MALT: false
   motus: false
+  metaphlan: false
 
 table_columns_name:
   FastQC / Falco (pre-Trimming):

@@ -21,7 +21,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [Porechop](#porechop) - Adapter removal for Oxford Nanopore data
 - [Porechop_ABI](#porechop_abi) - Adapter removal for Oxford Nanopore data
 - [Filtlong](#filtlong) - Quality trimming and filtering for Nanopore data
-- [Nanoq] (#nanoq) - Quality trimming and filtering for Nanopore data
+- [Nanoq](#nanoq) - Quality trimming and filtering for Nanopore data
 - [Bowtie2](#bowtie2) - Host removal for Illumina reads
 - [minimap2](#minimap2) - Host removal for Nanopore reads
 - [SAMtools stats](#samtools-stats) - Statistics from host removal
@@ -713,6 +713,7 @@ You can expect in the MultiQC reports either sections and/or general stats colum
 - diamond
 - malt
 - motus
+- metaphlan
 
 :::info
 The 'General Stats' table by default will only show statistics referring to pre-processing steps, and will not display possible values from each classifier/profiler, unless turned on by the user within the 'Configure Columns' menu or via a custom MultiQC config file (`--multiqc_config`).

@@ -311,6 +311,8 @@ workflow PROFILING {
         METAPHLAN_METAPHLAN ( ch_input_for_metaphlan.reads, ch_input_for_metaphlan.db )
         ch_versions        = ch_versions.mix( METAPHLAN_METAPHLAN.out.versions.first() )
         ch_raw_profiles    = ch_raw_profiles.mix( METAPHLAN_METAPHLAN.out.profile )
+        ch_multiqc_files   = ch_multiqc_files.mix( METAPHLAN_METAPHLAN.out.profile )
+
 
     }