Reorganize the ARG detection learning pathway

learning-pathways/amr-gene-detection.md

@@ -2,7 +2,7 @@
 layout: learning-pathway
 title: Detection of AMR genes in bacterial genomes
 description: |
-  Learn how to identify AMR genes in bacterial genomes
+  This learning path aims to teach you the basic steps to detect and check Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy.
 type: use
 tags: [amr, bacteria, microgalaxy, one-health]
 
@@ -11,7 +11,6 @@ editorial_board:
 funding:
 - abromics
 
-
 pathway:
 #  - section: "Module 1: Introduction"
 #    description: |
@@ -20,33 +19,38 @@ pathway:
 #    #  - name: introduction
 #    #    topic: genome-annotation
 
-  - section: "Module: AMR gene detection in bacterial isolates (short reads)"
+#  - section: "Module: Taxonomy assignation"
+#    description: |
+#      Taxonomic assignation is useful in AMR detection to check contamination and confirm species
+#    tutorials:
+#      - name: taxonomy
+#        topic: ecology
+
+  - section: "Module: Assembly"
     description: |
-      
+      Assembly is a major step in the process to detect AMR genes as it combines sequenced reads into contigs, longer sequences where it will be easier to identify genes and in particular AMR genes
     tutorials:
       - name: mrsa-illumina
         topic: assembly
-      - name: amr-gene-detection
-        topic: genome-annotation
-
-#  - section: "Module 3: AMR gene detection in bacterial isolates (long reads)"
-#    description: |
-#      
-#    tutorials:
 #      - name: mrsa-nanopore
 #        topic: assembly
-#      - name: amr-gene-detection
-#        topic: genome-annotation
-#
-#  - section: "Module 4: AMR gene detection in bacterial isolates (long and short reads)"
+#      - name: hybrid-assembly
+#        topic: assembly
+
+#  - section: "Module: Genome annotation"
 #    description: |
-#      
+#      The generated contigs can be then annotated to detect genes, potential plasmid, etc. This will help the AMR gene detection process, specially the verification and the visualization
 #    tutorials:
-#      #- name: hybrid-assembly
-#      #  topic: assembly
-#      - name: amr-gene-detection
+#      - name: bacterial-genome-annotation
 #        topic: genome-annotation
 
+  - section: "Module: AMR gene detection"
+    description: |
+      
+    tutorials:
+      - name: amr-gene-detection
+        topic: genome-annotation
+
   - section: "Recommended follow-up tutorials"
     tutorials:
       - name: pathogen-detection-from-nanopore-foodborne-data