Foldmason topics migration & bumpversion

modules/nf-core/foldmason/createdb/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::foldmason=2.7bd21ed
+  - bioconda::foldmason=4.dd3c235-0

modules/nf-core/foldmason/createdb/main.nf

@@ -4,15 +4,15 @@ process FOLDMASON_CREATEDB {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-            'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a8/a88d162c3f39a1518d48c3faec235e6fcde750586da868b62fc5f0a08a89aa9d/data' :
-            'community.wave.seqera.io/library/foldmason:2.7bd21ed--e7f739473ad6578d' }"
+            'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/dc/dc0b27a73277c851f0a1df09fc5fa4f0ff80832e6779f143420a7e2321ac62b4/data' :
+            'community.wave.seqera.io/library/foldmason:4.dd3c235--375019dcc3c5fe6f' }"
 
     input:
     tuple val(meta) , path(structures)
 
     output:
     tuple val(meta), path("${prefix}*"), emit: db
-    path "versions.yml"                , emit: versions
+    tuple val("${task.process}"), val('foldmason'), eval('foldmason version'), emit: versions_foldmason, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,21 +26,11 @@ process FOLDMASON_CREATEDB {
         ${prefix} \\
         $args \\
         --threads $task.cpus
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}')
-    END_VERSIONS
     """
 
     stub:
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}')
-    END_VERSIONS
     """
 }

modules/nf-core/foldmason/createdb/meta.yml

@@ -12,9 +12,9 @@ tools:
       documentation: "https://github.com/steineggerlab/foldmason"
       tool_dev_url: "https://github.com/steineggerlab/foldmason"
       doi: "10.1101/2024.08.01.606130"
-      licence: ["GPL v3"]
+      licence:
+        - "GPL v3"
       identifier: biotools:foldmason
-
 input:
   - - meta:
         type: map
@@ -25,7 +25,6 @@ input:
         type: file
         description: Input protein structures in `PDB` or `mmCIF` format.
         pattern: "*.{pdb,mmcif}"
-
         ontologies: []
 output:
   db:
@@ -39,13 +38,27 @@ output:
           description: All database files created by Foldmason
           pattern: "*"
           ontologies: []
+  versions_foldmason:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - foldmason:
+          type: string
+          description: The name of the tool
+      - foldmason version:
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - foldmason:
+          type: string
+          description: The name of the tool
+      - foldmason version:
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@luisas"
 maintainers:

modules/nf-core/foldmason/createdb/tests/main.nf.test.snap

@@ -26,7 +26,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45"
+                    [
+                        "FOLDMASON_CREATEDB",
+                        "foldmason",
+                        "4.dd3c235"
+                    ]
                 ],
                 "db": [
                     [
@@ -51,16 +55,20 @@
                         ]
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45"
+                "versions_foldmason": [
+                    [
+                        "FOLDMASON_CREATEDB",
+                        "foldmason",
+                        "4.dd3c235"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-03-26T19:09:16.242972",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
-        },
-        "timestamp": "2024-12-09T15:11:27.426024133"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "seatoxin": {
         "content": [
@@ -89,7 +97,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45"
+                    [
+                        "FOLDMASON_CREATEDB",
+                        "foldmason",
+                        "4.dd3c235"
+                    ]
                 ],
                 "db": [
                     [
@@ -114,15 +126,19 @@
                         ]
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45"
+                "versions_foldmason": [
+                    [
+                        "FOLDMASON_CREATEDB",
+                        "foldmason",
+                        "4.dd3c235"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-03-26T19:09:08.916379",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
-        },
-        "timestamp": "2024-12-09T15:11:15.375341633"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }

modules/nf-core/foldmason/easymsa/environment.yml

@@ -4,5 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::foldmason=2.7bd21ed
+  - bioconda::foldmason=4.dd3c235-0
   - conda-forge::pigz=2.8

modules/nf-core/foldmason/easymsa/main.nf

@@ -4,8 +4,8 @@ process FOLDMASON_EASYMSA {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-            'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/06/067e6389ab95497b753ba1deabaa6acbce25b99c8cfcf39c06d5c1af42fd7751/data':
-            'community.wave.seqera.io/library/foldmason_pigz:88809eb5649534b0' }"
+            'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/29/299b6d1a8a81632118e9c0cd110f9d89aae58b5a0132543a7fedbecb656da570/data':
+            'community.wave.seqera.io/library/foldmason_pigz:289a5a7a978299df' }"
 
 
     input: