Bump openms version, update snapshots (#9282)

bump openms version

Author: jonasscheid

modules/nf-core/openms/decoydatabase/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::openms=3.4.0
+  - bioconda::openms=3.4.1

modules/nf-core/openms/decoydatabase/main.nf

@@ -4,8 +4,8 @@ process OPENMS_DECOYDATABASE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.4.0--hc77a4c7_0' :
-        'biocontainers/openms:3.4.0--hc77a4c7_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.4.1--h81ffffe_1' :
+        'biocontainers/openms:3.4.1--h81ffffe_1' }"
 
     input:
     tuple val(meta), path(fasta)

modules/nf-core/openms/decoydatabase/tests/main.nf.test.snap

@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b0d04a10e7ff432572002175d1a67304"
+                    "versions.yml:md5,3faa02db1ca8efaa13ffb542d3a418f0"
                 ],
                 "decoy_fasta": [
                     [
@@ -22,14 +22,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b0d04a10e7ff432572002175d1a67304"
+                    "versions.yml:md5,3faa02db1ca8efaa13ffb542d3a418f0"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
         },
-        "timestamp": "2025-05-11T06:06:13.820720463"
+        "timestamp": "2025-10-28T07:59:28.940912845"
     }
 }

modules/nf-core/openms/filefilter/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::openms=3.4.0"
+  - "bioconda::openms=3.4.1"

modules/nf-core/openms/filefilter/main.nf

@@ -4,8 +4,8 @@ process OPENMS_FILEFILTER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.4.0--hc77a4c7_0' :
-        'biocontainers/openms:3.4.0--hc77a4c7_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.4.1--h81ffffe_1' :
+        'biocontainers/openms:3.4.1--h81ffffe_1' }"
 
     input:
     tuple val(meta), path(file)

modules/nf-core/openms/filefilter/tests/main.nf.test.snap

@@ -43,7 +43,7 @@
 
                 ],
                 "3": [
-                    "versions.yml:md5,9d201e84f5ae42d6c618d7537c4cf4d6"
+                    "versions.yml:md5,1ea875205d6d20aea4dabd5e580f4d6a"
                 ],
                 "consensusxml": [
 
@@ -60,14 +60,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,9d201e84f5ae42d6c618d7537c4cf4d6"
+                    "versions.yml:md5,1ea875205d6d20aea4dabd5e580f4d6a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
         },
-        "timestamp": "2025-05-11T06:07:23.763837266"
+        "timestamp": "2025-10-27T13:03:04.483705593"
     }
 }

modules/nf-core/openms/idfilter/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::openms=3.4.0"
+  - "bioconda::openms=3.4.1"

modules/nf-core/openms/idfilter/main.nf

@@ -4,8 +4,8 @@ process OPENMS_IDFILTER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.4.0--hc77a4c7_0' :
-        'biocontainers/openms:3.4.0--hc77a4c7_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.4.1--h81ffffe_1' :
+        'biocontainers/openms:3.4.1--h81ffffe_1' }"
 
     input:
     tuple val(meta), path(id_file), path(filter_file)

modules/nf-core/openms/idfilter/tests/main.nf.test.snap

@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,3ea19989645a1b3ac731c5cf7c6bfc0a"
+                    "versions.yml:md5,992aca62fe3990b1ebb21d11e999dd67"
                 ],
                 "filtered": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3ea19989645a1b3ac731c5cf7c6bfc0a"
+                    "versions.yml:md5,992aca62fe3990b1ebb21d11e999dd67"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
         },
-        "timestamp": "2025-05-11T06:07:37.369646607"
+        "timestamp": "2025-10-28T08:37:44.032335833"
     },
     "proteomics - filter - idxml": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,3ea19989645a1b3ac731c5cf7c6bfc0a"
+                    "versions.yml:md5,992aca62fe3990b1ebb21d11e999dd67"
                 ],
                 "filtered": [
                     [
@@ -55,14 +55,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3ea19989645a1b3ac731c5cf7c6bfc0a"
+                    "versions.yml:md5,992aca62fe3990b1ebb21d11e999dd67"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
         },
-        "timestamp": "2025-05-11T06:07:30.918596859"
+        "timestamp": "2025-10-28T08:37:18.617593794"
     }
 }

modules/nf-core/openms/idmassaccuracy/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::openms=3.4.0"
+  - "bioconda::openms=3.4.1"