diff --git a/modules/nf-core/chromap/chromap/meta.yml b/modules/nf-core/chromap/chromap/meta.yml
index be9c6bb5ecfc..a1bf6eca8e1d 100644
--- a/modules/nf-core/chromap/chromap/meta.yml
+++ b/modules/nf-core/chromap/chromap/meta.yml
@@ -41,14 +41,16 @@ input:
           e.g. [ id:'test' ]
     - fasta:
         type: file
-        description: |
-          The fasta reference file.
-        ontologies: []
+        description: Reference genome FASTA file
+        pattern: "*.{fa,fasta,fna}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929"
     - fai:
         type: file
-        description: |
-          The fasta reference index file.
-        ontologies: []
+        description: Reference genome FASTA index file
+        pattern: "*.{fai}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3326"
   - - meta3:
         type: map
         description: |
diff --git a/modules/nf-core/chromap/index/meta.yml b/modules/nf-core/chromap/index/meta.yml
index 1684807a210c..effbe025dafb 100644
--- a/modules/nf-core/chromap/index/meta.yml
+++ b/modules/nf-core/chromap/index/meta.yml
@@ -22,12 +22,16 @@ input:
           e.g. [ id:'test' ]
     - fasta:
         type: file
-        description: Fasta reference file.
-        ontologies: []
+        description: Reference genome FASTA file
+        pattern: "*.{fa,fasta,fna}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929"
     - fai:
         type: file
-        description: Fasta reference index file.
-        ontologies: []
+        description: Reference genome FASTA index file
+        pattern: "*.{fai}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3326"
 output:
   index:
     - - meta: