Merge pull request #1088 from hugolefeuvre/genes_catalogue_1.2

Update metagenomics-genes-catalogue WF to 1.2 adding conditionnal AMR genes catalogue

Author: mvdbeek

workflows/microbiome/metagenomic-genes-catalogue/CHANGELOG.md

@@ -1,8 +1,20 @@
 # Changelog
 
+## [1.2] - 2025-01-13
+
+### Automatic update
+
+* `toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/2.2.3+galaxy0` should be updated to `toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/2.2.3+galaxy1`
+
+### Added
+
+* Addition of a Boolean variable allowing users to choose whether users want a full genes catalog analysis or one specific to antibiotic resistance.
+* Added a workflow to retrieve the contig IDs and CDSs of antibiotic resistance genes, and to filter genes present on the same contigs as antibiotic resistance genes (if the Boolean value is False).
+
 ## [1.1] - 2025-12-08
 
 ### Automatic update
+
 - `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy2`
 - `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy2`
 - `toolshed.g2.bx.psu.edu/repos/iuc/seqkit_translate/seqkit_translate/2.10.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/seqkit_translate/seqkit_translate/2.12.0+galaxy0`

workflows/microbiome/metagenomic-genes-catalogue/README.md

@@ -2,20 +2,33 @@
 
 This workflow generates genes catalogue from paired short reads.
 
-The workflow supports assembly using **MEGAHIT**.
+The workflow supports assembly using **MEGAHIT** and assembly quality control via **QUAST**.
 
 ## Genes catalogue Annotation and Quality Control
 
-After assembly, CDS are detected from resulting contigs with **Prodigal** and the potential genes are clustered with **MMseqs2linclust**
+After assembly, CDS are detected from resulting contigs with **Prodigal** 
 
-The following processing steps are then performed:
+Then, depending on your choice of Boolean, this will lead to two different analyses :
+
+If the **Boolean is True** for the complete genes catalog:
+
+All the potential genes are clustered with **MMseqs2linclust**
+
+The following processing steps are then performed on the full clustered genes catalogue :
 
 - **Genes annotation** with Eggnog-mapper
 - **Taxonomic Assignment** using MMseqs2taxonomy
-- **Assembly Quality Control** via QUAST
 - **Abundance Estimation** per sample with CoverM
 - **AMR detection** with ABRicate, AMRFinderPlus and starAMR
 
+If the **Boolean is False** for the complete genes catalog, a specific focus is placed on the functions and taxonomies associated with contigs on which an antibiotic resistance gene is detected.
+
+This will initiate the construction of a genes catalogue specific to **antibiotic resistance genes (ARGs)**.
+
+1. **AMR detection** with ABRicate, AMRFinderPlus and starAMR is performed on CDS predicted with **Prodigal.**
+2. **Taxonomic and functional annotation** will be performed on CDSs present on the same contig as the ARGs catalogue.
+3. **Clustering** is then performed on the detected ARGs, followed by **coverage** of this clustered ARGs catalog with the sample reads.
+
 ## Input Requirements
 
 Input reads must be quality-filtered, with host reads removed.

workflows/microbiome/metagenomic-genes-catalogue/metagenomic-genes-catalogue-tests.yml

@@ -17,19 +17,20 @@
     eggNOG database: 5.0.2
     mmseqs2 taxonomy DB: UniRef50-17-b804f-07112025
     starAMR database: staramr_downloaded_07042025_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502
-    Virulence genes detection database: vfdb
+    Virulence genes detection database: resfinder
     AMR genes detection database: amrfinderplus_V3.12_2024-05-02.2
+    Full genes catalogue: false
   outputs:
-    MMseqs2 Taxonomy Filtered:
+    MMseqs2 Taxonomy Tabular:
       asserts:
         has_text:
-          text: "domain"
+          text: "Bacteria"
         has_n_columns:
           n: 4
-    Eggnog Annotation Filtered:
+    Eggnog Annotations:
       asserts:
         has_text:
-          text: "Contig id"
+          text: "Beta-lactamase class A"
         has_n_columns:
           n: 21
     MMseqs2 Taxonomy Kraken:
@@ -60,37 +61,17 @@
           text: "#FILE"
         has_n_columns:
           n: 15
-    Amrfinderplus Report:
-      asserts:
-        has_text:
-          text: "Protein identifier"
-        has_n_columns:
-          n: 22
-    Tooldistillator Summarize Collection:
-      element_tests:
-        genes_catalogue_test:
-          asserts:
-            - that: has_text
-              text: "megahit_report"
-            - that: has_text
-              text: "quast_report"
-            - that: has_text
-              text: "prodigal_report"
-            - that: has_text
-              text: "coverm_report"
-    Tooldistillator Summarize Catalogue:
+    MultiQC Report:
       asserts:
-        - that: has_text
-          text: "eggnogmapper_report"
-        - that: has_text
-          text: "mmseqs2linclust_report"
-        - that: has_text
-          text: "staramr_report"
-        - that: has_text
-          text: "mmseqs2taxonomy_report"
-        - that: has_text
-          text: "abricate_report"
-        - that: has_text
-          text: "amrfinderplus_report"
-        - that: has_text
-          text: "argnorm_report"
+      - that: has_text
+        text: "AMRFinderPlus"
+      - that: has_text
+        text: "ABRicate"
+      - that: has_text
+        text: "starAMR"
+      - that: has_text
+        text: "QUAST"
+      - that: has_text
+        text: "MMseqs2 taxonomy"
+      - that: has_text
+        text: "EggnogMapper"