diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7fea0044..c09836ac 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,8 +11,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#501](https://github.com/nf-core/funcscan/pull/501) Fixed issue with BAKTA HMMs not being staged correctly (reported by Yusuke Hioki, fix by @jfy133)
+
 ### `Dependencies`
 
+| Tool  | Previous Version | New Version |
+| ----- | ---------------- | ----------- |
+| Bakta | 1.10.4           | 1.11.4      |
+
 ### `Deprecated`
 
 ## v3.0.0 - French Chocolatine - [2025-10-04]
diff --git a/conf/modules.config b/conf/modules.config
index 2812093b..61f71854 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -207,7 +207,6 @@ process {
             params.annotation_bakta_gap ? '' : '--skip-gap',
             params.annotation_bakta_ori ? '' : '--skip-ori',
             params.annotation_bakta_activate_plot ? '' : '--skip-plot',
-            params.annotation_bakta_hmms ? '--hmms ${params.annotation_bakta_hmms}' : '',
         ].join(' ').trim()
     }
 
diff --git a/modules.json b/modules.json
index eac420fd..2bff465f 100644
--- a/modules.json
+++ b/modules.json
@@ -62,12 +62,12 @@
                     },
                     "bakta/bakta": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "72c983560c9b9c2a02ff636451a5e5008f7d020b",
                         "installed_by": ["modules"]
                     },
                     "bakta/baktadbdownload": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "72c983560c9b9c2a02ff636451a5e5008f7d020b",
                         "installed_by": ["modules"]
                     },
                     "deeparg/downloaddata": {
diff --git a/modules/nf-core/bakta/bakta/environment.yml b/modules/nf-core/bakta/bakta/environment.yml
index c1b616a4..0640aa34 100644
--- a/modules/nf-core/bakta/bakta/environment.yml
+++ b/modules/nf-core/bakta/bakta/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bakta=1.10.4
+  - bioconda::bakta=1.11.4
diff --git a/modules/nf-core/bakta/bakta/main.nf b/modules/nf-core/bakta/bakta/main.nf
index 4d192e45..7de3cdc1 100644
--- a/modules/nf-core/bakta/bakta/main.nf
+++ b/modules/nf-core/bakta/bakta/main.nf
@@ -1,48 +1,55 @@
 process BAKTA_BAKTA {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bakta:1.10.4--pyhdfd78af_0' :
-        'biocontainers/bakta:1.10.4--pyhdfd78af_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/bakta:1.11.4--pyhdfd78af_0'
+        : 'biocontainers/bakta:1.11.4--pyhdfd78af_0'}"
 
     input:
     tuple val(meta), path(fasta)
     path db
     path proteins
     path prodigal_tf
+    path regions
+    path hmms
 
     output:
-    tuple val(meta), path("${prefix}.embl")             , emit: embl
-    tuple val(meta), path("${prefix}.faa")              , emit: faa
-    tuple val(meta), path("${prefix}.ffn")              , emit: ffn
-    tuple val(meta), path("${prefix}.fna")              , emit: fna
-    tuple val(meta), path("${prefix}.gbff")             , emit: gbff
-    tuple val(meta), path("${prefix}.gff3")             , emit: gff
+    tuple val(meta), path("${prefix}.embl"), emit: embl
+    tuple val(meta), path("${prefix}.faa"), emit: faa
+    tuple val(meta), path("${prefix}.ffn"), emit: ffn
+    tuple val(meta), path("${prefix}.fna"), emit: fna
+    tuple val(meta), path("${prefix}.gbff"), emit: gbff
+    tuple val(meta), path("${prefix}.gff3"), emit: gff
     tuple val(meta), path("${prefix}.hypotheticals.tsv"), emit: hypotheticals_tsv
     tuple val(meta), path("${prefix}.hypotheticals.faa"), emit: hypotheticals_faa
-    tuple val(meta), path("${prefix}.tsv")              , emit: tsv
-    tuple val(meta), path("${prefix}.txt")              , emit: txt
-    path "versions.yml"                                 , emit: versions
+    tuple val(meta), path("${prefix}.tsv"), emit: tsv
+    tuple val(meta), path("${prefix}.txt"), emit: txt
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args   ?: ''
-    prefix   = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
     def proteins_opt = proteins ? "--proteins ${proteins[0]}" : ""
-    def prodigal_tf = prodigal_tf ? "--prodigal-tf ${prodigal_tf[0]}" : ""
+    def prodigal_tf_opt = prodigal_tf ? "--prodigal-tf ${prodigal_tf[0]}" : ""
+    def regions_opt = regions ? "--regions ${regions}" : ""
+    def hmms_opt = hmms ? "--hmms ${hmms}" : ""
+
     """
     bakta \\
-        $fasta \\
-        $args \\
-        --threads $task.cpus \\
-        --prefix $prefix \\
-        $proteins_opt \\
-        $prodigal_tf \\
-        --db $db
+        ${fasta} \\
+        ${args} \\
+        --threads ${task.cpus} \\
+        --prefix ${prefix} \\
+        ${proteins_opt} \\
+        ${prodigal_tf_opt} \\
+        ${regions_opt} \\
+        ${hmms_opt} \\
+        --db ${db}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/bakta/bakta/meta.yml b/modules/nf-core/bakta/bakta/meta.yml
index 7d734f28..1944fbb1 100644
--- a/modules/nf-core/bakta/bakta/meta.yml
+++ b/modules/nf-core/bakta/bakta/meta.yml
@@ -23,19 +23,42 @@ input:
         type: file
         description: |
           FASTA file to be annotated. Has to contain at least a non-empty string dummy value.
-  - - db:
-        type: file
-        description: |
-          Path to the Bakta database. Must have amrfinderplus database directory already installed within it (in a directory called 'amrfinderplus-db/').
-  - - proteins:
-        type: file
-        description: FASTA/GenBank file of trusted proteins to first annotate from (optional)
-  - - prodigal_tf:
-        type: file
-        description: Training file to use for Prodigal (optional)
+        pattern: "*.{fa,fas,fna,fasta}"
+        ontologies:
+          - edam: http://edamontology.org/format_1929 # FASTA
+  - db:
+      type: file
+      description: |
+        Path to the Bakta database directory. Must have amrfinderplus database directory already installed within it (in a directory called 'amrfinderplus-db/').
+      ontologies:
+        - edam: http://edamontology.org/data_1049 ## Directory name
+  - proteins:
+      type: file
+      description: FASTA/GenBank file of trusted proteins to first annotate from (optional)
+      pattern: "*.{fa,fas,fna,fasta,faa}"
+      ontologies:
+        - edam: http://edamontology.org/format_1929 # FASTA
+  - prodigal_tf:
+      type: file
+      description: Training file to use for Prodigal for CDS prediction(optional)
+      pattern: "*.{tf,trn}"
+      ontologies:
+        - edam: http://edamontology.org/format_2333 # Binary format
+  - regions:
+      type: file
+      description: GFF3 or GenBank file of pre-annotated regions (optional)
+      pattern: "*.{gbff,gff3}"
+      ontologies:
+        - edam: http://edamontology.org/format_2206 # Sequence feature table format (text)
+  - hmms:
+      type: file
+      description: HMM database file for custom annotation (optional)
+      pattern: "*.hmm"
+      ontologies:
+        - edam: http://edamontology.org/format_1370 # HMMER database format
 output:
-  - embl:
-      - meta:
+  embl:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -44,8 +67,10 @@ output:
           type: file
           description: annotations & sequences in (multi) EMBL format
           pattern: "*.embl"
-  - faa:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_1927 # EMBL format
+  faa:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -54,8 +79,10 @@ output:
           type: file
           description: CDS/sORF amino acid sequences as FASTA
           pattern: "*.faa"
-  - ffn:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_1929 # FASTA
+  ffn:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -64,8 +91,11 @@ output:
           type: file
           description: feature nucleotide sequences as FASTA
           pattern: "*.ffn"
-  - fna:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_1929 # FASTA
+
+  fna:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -74,8 +104,10 @@ output:
           type: file
           description: replicon/contig DNA sequences as FASTA
           pattern: "*.fna"
-  - gbff:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_1929 # FASTA
+  gbff:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -84,8 +116,10 @@ output:
           type: file
           description: annotations & sequences in (multi) GenBank format
           pattern: "*.gbff"
-  - gff:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_1936 # GenBank format
+  gff:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -94,19 +128,23 @@ output:
           type: file
           description: annotations & sequences in GFF3 format
           pattern: "*.gff3"
-  - hypotheticals_tsv:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_1975 # GFF3 format
+  hypotheticals_tsv:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
       - ${prefix}.hypotheticals.tsv:
           type: file
-          description: additional information on hypothetical protein CDS as simple human
-            readable tab separated values
+          description: additional information on hypothetical protein CDS as simple
+            human readable tab separated values
           pattern: "*.hypotheticals.tsv"
-  - hypotheticals_faa:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  hypotheticals_faa:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -115,8 +153,10 @@ output:
           type: file
           description: hypothetical protein CDS amino acid sequences as FASTA
           pattern: "*.hypotheticals.faa"
-  - tsv:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_1929 # FASTA
+  tsv:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -125,8 +165,10 @@ output:
           type: file
           description: annotations as simple human readable tab separated values
           pattern: "*.tsv"
-  - txt:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  txt:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -135,11 +177,15 @@ output:
           type: file
           description: genome statistics and annotation summary
           pattern: "*.txt"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@rpetit3"
   - "@oschwengers"
diff --git a/modules/nf-core/bakta/bakta/tests/main.nf.test b/modules/nf-core/bakta/bakta/tests/main.nf.test
index 3c1f8f82..29a5b39d 100644
--- a/modules/nf-core/bakta/bakta/tests/main.nf.test
+++ b/modules/nf-core/bakta/bakta/tests/main.nf.test
@@ -33,6 +33,8 @@ nextflow_process {
                 input[1] = BAKTA_BAKTADBDOWNLOAD.out.db
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
@@ -67,6 +69,8 @@ nextflow_process {
                 input[1] = []
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
diff --git a/modules/nf-core/bakta/bakta/tests/main.nf.test.snap b/modules/nf-core/bakta/bakta/tests/main.nf.test.snap
index cee06343..5bc75a3e 100644
--- a/modules/nf-core/bakta/bakta/tests/main.nf.test.snap
+++ b/modules/nf-core/bakta/bakta/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "versions": {
         "content": [
             [
-                "versions.yml:md5,c40bd66294f6eb4520f194325ef24f24"
+                    "versions.yml:md5,39d76e345cee9a020d2109d1891c3c0b"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-01-25T11:59:09.981137"
+        "timestamp": "2025-10-22T11:18:34.505077069"
     },
     "Bakta - stub": {
         "content": [
@@ -31,7 +31,7 @@
                     ]
                 ],
                 "10": [
-                    "versions.yml:md5,c40bd66294f6eb4520f194325ef24f24"
+                    "versions.yml:md5,39d76e345cee9a020d2109d1891c3c0b"
                 ],
                 "2": [
                     [
@@ -178,14 +178,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c40bd66294f6eb4520f194325ef24f24"
+                    "versions.yml:md5,39d76e345cee9a020d2109d1891c3c0b"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-01-25T11:09:05.864545"
+        "timestamp": "2025-10-22T11:11:23.220239457"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bakta/bakta/tests/tags.yml b/modules/nf-core/bakta/bakta/tests/tags.yml
deleted file mode 100644
index ecb08c45..00000000
--- a/modules/nf-core/bakta/bakta/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-bakta/bakta:
-  - "modules/nf-core/bakta/bakta/**"
diff --git a/modules/nf-core/bakta/baktadbdownload/environment.yml b/modules/nf-core/bakta/baktadbdownload/environment.yml
index c1b616a4..0640aa34 100644
--- a/modules/nf-core/bakta/baktadbdownload/environment.yml
+++ b/modules/nf-core/bakta/baktadbdownload/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bakta=1.10.4
+  - bioconda::bakta=1.11.4
diff --git a/modules/nf-core/bakta/baktadbdownload/main.nf b/modules/nf-core/bakta/baktadbdownload/main.nf
index cc2f445e..36a172b0 100644
--- a/modules/nf-core/bakta/baktadbdownload/main.nf
+++ b/modules/nf-core/bakta/baktadbdownload/main.nf
@@ -2,13 +2,13 @@ process BAKTA_BAKTADBDOWNLOAD {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bakta:1.10.4--pyhdfd78af_0' :
-        'biocontainers/bakta:1.10.4--pyhdfd78af_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/bakta:1.11.4--pyhdfd78af_0'
+        : 'biocontainers/bakta:1.11.4--pyhdfd78af_0'}"
 
     output:
-    path "db*"              , emit: db
-    path "versions.yml"     , emit: versions
+    path "db*", emit: db
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -18,7 +18,7 @@ process BAKTA_BAKTADBDOWNLOAD {
     """
     bakta_db \\
         download \\
-        $args
+        ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -31,7 +31,7 @@ process BAKTA_BAKTADBDOWNLOAD {
     """
     echo "bakta_db \\
         download \\
-        $args"
+        ${args}"
 
     mkdir db
 
diff --git a/modules/nf-core/bakta/baktadbdownload/meta.yml b/modules/nf-core/bakta/baktadbdownload/meta.yml
index a0a3a455..103d38ff 100644
--- a/modules/nf-core/bakta/baktadbdownload/meta.yml
+++ b/modules/nf-core/bakta/baktadbdownload/meta.yml
@@ -17,16 +17,18 @@ tools:
       licence: ["GPL v3"]
       identifier: biotools:bakta
 output:
-  - db:
-      - db*:
-          type: directory
-          description: BAKTA database directory
-          pattern: "db*/"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+  db:
+    - db*:
+        type: directory
+        description: BAKTA database directory
+        pattern: "db*/"
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@jfy133"
   - "@jasmezz"
diff --git a/modules/nf-core/bakta/baktadbdownload/tests/main.nf.test.snap b/modules/nf-core/bakta/baktadbdownload/tests/main.nf.test.snap
index ef6aabe7..0d6e2aac 100644
--- a/modules/nf-core/bakta/baktadbdownload/tests/main.nf.test.snap
+++ b/modules/nf-core/bakta/baktadbdownload/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "Bakta database download": {
         "content": [
             [
-                "versions.yml:md5,29d6ec77dc88492b2c53141e6541c289"
+                "versions.yml:md5,e6f280a0deb9981dbf7f1d6270ab0908"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-01-25T12:30:51.853371"
+        "timestamp": "2025-10-22T11:28:20.601164502"
     },
     "Bakta database download - stub": {
         "content": [
@@ -17,13 +17,13 @@
                 [
                     
                 ],
-                "versions.yml:md5,29d6ec77dc88492b2c53141e6541c289"
+                "versions.yml:md5,e6f280a0deb9981dbf7f1d6270ab0908"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-01-25T12:31:08.390845"
+        "timestamp": "2025-10-22T11:28:26.466451602"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bakta/baktadbdownload/tests/tags.yml b/modules/nf-core/bakta/baktadbdownload/tests/tags.yml
deleted file mode 100644
index c469fa48..00000000
--- a/modules/nf-core/bakta/baktadbdownload/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-bakta/baktadbdownload:
-  - "modules/nf-core/bakta/baktadbdownload/**"
diff --git a/subworkflows/local/annotation.nf b/subworkflows/local/annotation.nf
index a59fe561..5e576631 100644
--- a/subworkflows/local/annotation.nf
+++ b/subworkflows/local/annotation.nf
@@ -71,8 +71,7 @@ workflow ANNOTATION {
 
         // BAKTA prepare download
         if (params.annotation_bakta_db) {
-            ch_bakta_db = Channel
-                .fromPath(params.annotation_bakta_db, checkIfExists: true)
+            ch_bakta_db = Channel.fromPath(params.annotation_bakta_db, checkIfExists: true)
                 .first()
         }
         else {
@@ -81,7 +80,22 @@ workflow ANNOTATION {
             ch_bakta_db = BAKTA_BAKTADBDOWNLOAD.out.db
         }
 
-        BAKTA_BAKTA(fasta, ch_bakta_db, [], [])
+        // BAKTA HMM download
+        if (params.annotation_bakta_hmms) {
+            ch_bakta_hmm = Channel.fromPath(params.annotation_bakta_hmms, checkIfExists: true).first()
+        }
+        else {
+            ch_bakta_hmm = []
+        }
+
+        BAKTA_BAKTA(
+            fasta,
+            ch_bakta_db,
+            [],
+            [],
+            [],
+            ch_bakta_hmm,
+        )
         ch_versions = ch_versions.mix(BAKTA_BAKTA.out.versions)
         ch_multiqc_files = BAKTA_BAKTA.out.txt.collect { it[1] }.ifEmpty([])
         ch_annotation_faa = BAKTA_BAKTA.out.faa