Update neoantigen.md

Author: subinamehta

learning-pathways/neoantigen.md

@@ -16,49 +16,49 @@ editorial_board:
 - subinamehta
 
 pathway:
-  - section: "Module 1: Fusion-Database Generation"
+  - section: "Module 1a: Fusion-Database Generation"
     description: |
       Learn how to generate a personalized fusion peptide database using RNA-seq data. This step sets the foundation for identifying tumor-specific fusion peptides in downstream analyses.
     tutorials:
       - name: neoantigen-1-fusion-database-generation
         topic: proteomics
 
-  - section: "Module 2: Non-Reference Database Generation"
+  - section: "Module 1b: Non-Reference Database Generation"
     description: |
       Construct a non-reference proteogenomic database incorporating somatic mutations, indels, and other genomic alterations from VCF data.
     tutorials:
       - name: neoantigen-2-non-reference-database-generation
         topic: proteomics
 
-  - section: "Module 3: Database Merge and FragPipe Discovery"
+  - section: "Module 2: Database Merge and FragPipe Discovery"
     description: |
       Merge the fusion and non-reference databases, then use FragPipe for mass spectrometry-based discovery of putative neopeptides.
     tutorials:
       - name: neoantigen-3-fragpipe-discovery
         topic: proteomics
 
-  - section: "Module 4: PepQuery2 Verification"
+  - section: "Module 3: PepQuery2 Verification"
     description: |
       Perform targeted verification of neoantigen candidates using PepQuery2 for peptide-spectrum match validation.
     tutorials:
       - name: neoantigen-4-peptide-verification
         topic: proteomics
 
-  - section: "Module 5: Variant Annotation"
+  - section: "Module 4: Variant Annotation"
     description: |
       Annotate validated neopeptides with their corresponding genomic variants and protein context.
     tutorials:
       - name: neoantigen-5-variant-annotation
         topic: proteomics
 
-  - section: "Module 6: Predicting HLA Binding"
+  - section: "Module 5a: Predicting HLA Binding"
     description: |
       Predict MHC binding affinity of validated neopeptides using tools such as NetMHCpan or similar.
     tutorials:
       - name: neoantigen-6-predicting-hla-binding
         topic: proteomics
 
-  - section: "Module 7: IEDB Binding of PepQuery Validated Neopeptides"
+  - section: "Module 5b: IEDB Binding of PepQuery Validated Neopeptides"
     description: |
       Assess the immunogenic potential of neopeptides by checking their binding predictions against immune epitope databases such as IEDB.
     tutorials: