diff --git a/modules/nf-core/tcoffee/regressive/meta.yml b/modules/nf-core/tcoffee/regressive/meta.yml
index a272190f7e00..fa7a752e6937 100644
--- a/modules/nf-core/tcoffee/regressive/meta.yml
+++ b/modules/nf-core/tcoffee/regressive/meta.yml
@@ -30,7 +30,9 @@ input:
         type: file
         description: Input sequences in FASTA format
         pattern: "*.{fa,fasta}"
-        ontologies: []
+        ontologies:
+          - edam: http://edamontology.org/format_1919 # SEQUENCE-LIKE
+          - edam: http://edamontology.org/format_1929 # FASTA
   - - meta2:
         type: map
         description: |
@@ -40,7 +42,8 @@ input:
         type: file
         description: Input guide tree in Newick format
         pattern: "*.{dnd}"
-        ontologies: []
+        ontologies:
+          - edam: http://edamontology.org/format_2006 # PHYLOGENETIC TREE
   - - meta3:
         type: map
         description: |
@@ -50,14 +53,14 @@ input:
         type: file
         description: T_coffee template file that maps sequences to the accessory information
           files to be used.
-        pattern: "*"
-        ontologies: []
+        ontologies:
+          - edam: http://edamontology.org/format_1476 # PDB
     - accessory_information:
         type: file
         description: Accessory files to be used in the alignment. For example, it could
           be protein structures or secondary structures.
-        pattern: "*"
-        ontologies: []
+        ontologies:
+          - edam: http://edamontology.org/format_1476 # PDB
   - compress:
       type: boolean
       description: Flag representing whether the output MSA should be compressed. Set
@@ -74,7 +77,10 @@ output:
           type: file
           description: Alignment file in FASTA format. May be gzipped.
           pattern: "*.aln{.gz,}"
-          ontologies: []
+          ontologies:
+            - edam: http://edamontology.org/format_2554 # ALIGNMENT FORMAT TXT
+            - edam: http://edamontology.org/format_1921 # ALIGNMENT FORMAT
+            - edam: http://edamontology.org/format_1984 # FASTA-ALN
   versions:
     - versions.yml:
         type: file
diff --git a/modules/nf-core/upp/align/meta.yml b/modules/nf-core/upp/align/meta.yml
index fccbe366dec1..fa568f9acaaf 100644
--- a/modules/nf-core/upp/align/meta.yml
+++ b/modules/nf-core/upp/align/meta.yml
@@ -25,7 +25,9 @@ input:
         type: file
         description: Input sequences in FASTA format
         pattern: "*.{fa,fasta}"
-        ontologies: []
+        ontologies:
+          - edam: http://edamontology.org/format_1919 # SEQUENCE-LIKE
+          - edam: http://edamontology.org/format_1929 # FASTA
   - - meta2:
         type: map
         description: |
@@ -35,7 +37,8 @@ input:
         type: file
         description: Input guide tree in Newick format
         pattern: "*.{dnd}"
-        ontologies: []
+        ontologies:
+          - edam: http://edamontology.org/format_2006 # PHYLOGENETIC TREE
   - compress:
       type: boolean
       description: Flag representing whether the output MSA should be compressed. Set
@@ -52,7 +55,10 @@ output:
           description: Alignment file, in FASTA format. May be gzipped or uncompressed,
             depending on if compress is set to true or false
           pattern: "*.aln{.gz,}"
-          ontologies: []
+          ontologies:
+            - edam: http://edamontology.org/format_2554 # ALIGNMENT FORMAT TXT
+            - edam: http://edamontology.org/format_1921 # ALIGNMENT FORMAT
+            - edam: http://edamontology.org/format_1984 # FASTA-ALN
   versions:
     - versions.yml:
         type: file