Fix staging of custom HMMs for Bakta

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]

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()
     }
 

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": {