diff --git a/modules/nf-core/openms/decoydatabase/environment.yml b/modules/nf-core/openms/decoydatabase/environment.yml
index 31614292dbe..a65d15f44f5 100644
--- a/modules/nf-core/openms/decoydatabase/environment.yml
+++ b/modules/nf-core/openms/decoydatabase/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::openms=3.2.0
+  - bioconda::openms=3.3.0
diff --git a/modules/nf-core/openms/decoydatabase/main.nf b/modules/nf-core/openms/decoydatabase/main.nf
index 5c3a55ce341..4519f40eb55 100644
--- a/modules/nf-core/openms/decoydatabase/main.nf
+++ b/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:3.2.0--haddbca4_4' :
-        'biocontainers/openms:3.2.0--haddbca4_4' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.3.0--h0656172_8' :
+        'biocontainers/openms:3.3.0--h0656172_8' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/openms/decoydatabase/tests/main.nf.test b/modules/nf-core/openms/decoydatabase/tests/main.nf.test
index d0d5db211ea..5ca03a79c1d 100644
--- a/modules/nf-core/openms/decoydatabase/tests/main.nf.test
+++ b/modules/nf-core/openms/decoydatabase/tests/main.nf.test
@@ -18,7 +18,6 @@ nextflow_process {
                     [id:'test'],
                     file(params.modules_testdata_base_path + 'proteomics/database/yeast_UPS.fasta', checkIfExists: true)
                 ]
-
                 """
             }
         }
@@ -29,7 +28,5 @@ nextflow_process {
                 { assert snapshot(process.out).match() }
             )
         }
-
     }
-
 }
diff --git a/modules/nf-core/openms/decoydatabase/tests/main.nf.test.snap b/modules/nf-core/openms/decoydatabase/tests/main.nf.test.snap
index 699b8c2d8ef..ff0bdf5250e 100644
--- a/modules/nf-core/openms/decoydatabase/tests/main.nf.test.snap
+++ b/modules/nf-core/openms/decoydatabase/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,6c32e4ec0949f616baefa1b17efbe426"
+                    "versions.yml:md5,da0a498551f58bedc67c2ff26cc99f54"
                 ],
                 "decoy_fasta": [
                     [
@@ -22,14 +22,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6c32e4ec0949f616baefa1b17efbe426"
+                    "versions.yml:md5,da0a498551f58bedc67c2ff26cc99f54"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-08T11:22:32.701406062"
+        "timestamp": "2025-01-27T09:32:00.741200995"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/openms/filefilter/environment.yml b/modules/nf-core/openms/filefilter/environment.yml
index 5ec74436391..6c42dcb14bc 100644
--- a/modules/nf-core/openms/filefilter/environment.yml
+++ b/modules/nf-core/openms/filefilter/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::openms=3.2.0"
+  - "bioconda::openms=3.3.0"
diff --git a/modules/nf-core/openms/filefilter/main.nf b/modules/nf-core/openms/filefilter/main.nf
index 51aeff7b793..6951f8551cc 100644
--- a/modules/nf-core/openms/filefilter/main.nf
+++ b/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:3.2.0--haddbca4_4' :
-        'biocontainers/openms:3.2.0--haddbca4_4' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.3.0--h0656172_8' :
+        'biocontainers/openms:3.3.0--h0656172_8' }"
 
     input:
     tuple val(meta), path(file)
diff --git a/modules/nf-core/openms/filefilter/tests/main.nf.test.snap b/modules/nf-core/openms/filefilter/tests/main.nf.test.snap
index 61762bc2cc6..dff9e0fdafd 100644
--- a/modules/nf-core/openms/filefilter/tests/main.nf.test.snap
+++ b/modules/nf-core/openms/filefilter/tests/main.nf.test.snap
@@ -43,7 +43,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,a8ec8f78f4a0da0328482bf90dc2df00"
+                    "versions.yml:md5,2dbaab2d39324e978b6b63643b2adee6"
                 ],
                 "consensusxml": [
                     
@@ -60,14 +60,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,a8ec8f78f4a0da0328482bf90dc2df00"
+                    "versions.yml:md5,2dbaab2d39324e978b6b63643b2adee6"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-21T13:09:28.723787747"
+        "timestamp": "2025-01-27T09:52:55.262478412"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/openms/idfilter/environment.yml b/modules/nf-core/openms/idfilter/environment.yml
index 5ec74436391..6c42dcb14bc 100644
--- a/modules/nf-core/openms/idfilter/environment.yml
+++ b/modules/nf-core/openms/idfilter/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::openms=3.2.0"
+  - "bioconda::openms=3.3.0"
diff --git a/modules/nf-core/openms/idfilter/main.nf b/modules/nf-core/openms/idfilter/main.nf
index 763c2bf955d..be27554d3b4 100644
--- a/modules/nf-core/openms/idfilter/main.nf
+++ b/modules/nf-core/openms/idfilter/main.nf
@@ -2,10 +2,10 @@ process OPENMS_IDFILTER {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::openms=3.2.0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4' :
-        'biocontainers/openms:3.2.0--haddbca4_4' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.3.0--h0656172_8' :
+        'biocontainers/openms:3.3.0--h0656172_8' }"
 
     input:
     tuple val(meta), path(id_file), path(filter_file)
@@ -21,6 +21,7 @@ process OPENMS_IDFILTER {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def suffix = task.ext.suffix ?: "${id_file.getExtension()}"
+    if ("$file" == "${prefix}.${suffix}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     // Optional filtering via filter_file
     def filter_citerion = task.ext.args2 ?: "-whitelist:peptides"
     def filter = filter_file ? "${filter_citerion} ${filter_file}" : ""
@@ -42,6 +43,7 @@ process OPENMS_IDFILTER {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def suffix = task.ext.suffix ?: "${id_file.getExtension()}"
+    if ("$file" == "${prefix}.${suffix}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     // Optional filtering via filter_file
     def filter_citerion = task.ext.args2 ?: "-whitelist:peptides"
     def filter = filter_file ? "${filter_citerion} ${filter_file}" : ""
diff --git a/modules/nf-core/openms/idfilter/tests/main.nf.test.snap b/modules/nf-core/openms/idfilter/tests/main.nf.test.snap
index 0b74a186c17..9ff72d3cfd8 100644
--- a/modules/nf-core/openms/idfilter/tests/main.nf.test.snap
+++ b/modules/nf-core/openms/idfilter/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,8a95c69294e90ae931b766218dc87dec"
+                    "versions.yml:md5,d1e4fc495db4455433af0f1c9944fa4a"
                 ],
                 "filtered": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,8a95c69294e90ae931b766218dc87dec"
+                    "versions.yml:md5,d1e4fc495db4455433af0f1c9944fa4a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-08T11:45:00.758602574"
+        "timestamp": "2025-01-27T14:24:13.027097196"
     },
     "proteomics - filter - idxml": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,8a95c69294e90ae931b766218dc87dec"
+                    "versions.yml:md5,d1e4fc495db4455433af0f1c9944fa4a"
                 ],
                 "filtered": [
                     [
@@ -55,14 +55,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,8a95c69294e90ae931b766218dc87dec"
+                    "versions.yml:md5,d1e4fc495db4455433af0f1c9944fa4a"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-08T11:44:53.291545021"
+        "timestamp": "2025-01-27T14:24:01.067382973"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/openms/idmassaccuracy/environment.yml b/modules/nf-core/openms/idmassaccuracy/environment.yml
index 5ec74436391..6c42dcb14bc 100644
--- a/modules/nf-core/openms/idmassaccuracy/environment.yml
+++ b/modules/nf-core/openms/idmassaccuracy/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::openms=3.2.0"
+  - "bioconda::openms=3.3.0"
diff --git a/modules/nf-core/openms/idmassaccuracy/main.nf b/modules/nf-core/openms/idmassaccuracy/main.nf
index b1e8deac16b..794faa95478 100644
--- a/modules/nf-core/openms/idmassaccuracy/main.nf
+++ b/modules/nf-core/openms/idmassaccuracy/main.nf
@@ -4,8 +4,8 @@ process OPENMS_IDMASSACCURACY {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4' :
-        'biocontainers/openms:3.2.0--haddbca4_4' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.3.0--h0656172_8' :
+        'biocontainers/openms:3.3.0--h0656172_8' }"
 
     input:
     tuple val(meta), path(mzmls), path(idxmls)
diff --git a/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test.snap b/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test.snap
index c9f056e174f..11d1b867bb9 100644
--- a/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test.snap
+++ b/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test.snap
@@ -19,7 +19,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,9bf83a6db02732d209de6819818aed26"
+                    "versions.yml:md5,3ef5990b5bbae77d5faba3fead83814c"
                 ],
                 "frag_err": [
                     [
@@ -38,15 +38,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,9bf83a6db02732d209de6819818aed26"
+                    "versions.yml:md5,3ef5990b5bbae77d5faba3fead83814c"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-08T11:26:08.231171982"
+        "timestamp": "2025-01-27T09:38:35.753866654"
     },
     "proteomics - openms - mass_error": {
         "content": [
@@ -63,7 +63,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,9bf83a6db02732d209de6819818aed26"
+                    "versions.yml:md5,3ef5990b5bbae77d5faba3fead83814c"
                 ],
                 "frag_err": [
                     [
@@ -77,14 +77,14 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,9bf83a6db02732d209de6819818aed26"
+                    "versions.yml:md5,3ef5990b5bbae77d5faba3fead83814c"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-08T11:25:57.38948188"
+        "timestamp": "2025-01-27T09:38:24.74497273"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/openms/idmerger/environment.yml b/modules/nf-core/openms/idmerger/environment.yml
index 31614292dbe..a65d15f44f5 100644
--- a/modules/nf-core/openms/idmerger/environment.yml
+++ b/modules/nf-core/openms/idmerger/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::openms=3.2.0
+  - bioconda::openms=3.3.0
diff --git a/modules/nf-core/openms/idmerger/main.nf b/modules/nf-core/openms/idmerger/main.nf
index 62a7a506237..e357434b72e 100644
--- a/modules/nf-core/openms/idmerger/main.nf
+++ b/modules/nf-core/openms/idmerger/main.nf
@@ -4,8 +4,8 @@ process OPENMS_IDMERGER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4' :
-        'biocontainers/openms:3.2.0--haddbca4_4' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.3.0--h0656172_8' :
+        'biocontainers/openms:3.3.0--h0656172_8' }"
 
     input:
     tuple val(meta), path(idxmls)
diff --git a/modules/nf-core/openms/idmerger/tests/main.nf.test.snap b/modules/nf-core/openms/idmerger/tests/main.nf.test.snap
index fa034582afb..3274728e57c 100644
--- a/modules/nf-core/openms/idmerger/tests/main.nf.test.snap
+++ b/modules/nf-core/openms/idmerger/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "proteomics - openms - idxml": {
         "content": [
             [
-                "versions.yml:md5,8051ce1c0fe4404798507d607ebf52a3"
+                "versions.yml:md5,223c9352a3e79162fde8cbbf18e93e54"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-08T12:02:35.595648853"
+        "timestamp": "2025-01-27T09:56:47.184737888"
     },
     "proteomics - openms - idxml - stub": {
         "content": [
@@ -23,7 +23,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,8051ce1c0fe4404798507d607ebf52a3"
+                    "versions.yml:md5,223c9352a3e79162fde8cbbf18e93e54"
                 ],
                 "idxml": [
                     [
@@ -34,14 +34,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,8051ce1c0fe4404798507d607ebf52a3"
+                    "versions.yml:md5,223c9352a3e79162fde8cbbf18e93e54"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-08T12:02:42.76246364"
+        "timestamp": "2025-01-27T09:56:54.134223267"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/openms/idripper/environment.yml b/modules/nf-core/openms/idripper/environment.yml
index 5ec74436391..6c42dcb14bc 100644
--- a/modules/nf-core/openms/idripper/environment.yml
+++ b/modules/nf-core/openms/idripper/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::openms=3.2.0"
+  - "bioconda::openms=3.3.0"
diff --git a/modules/nf-core/openms/idripper/main.nf b/modules/nf-core/openms/idripper/main.nf
index 463afa25773..f38d9041b4f 100644
--- a/modules/nf-core/openms/idripper/main.nf
+++ b/modules/nf-core/openms/idripper/main.nf
@@ -4,8 +4,8 @@ process OPENMS_IDRIPPER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4':
-        'biocontainers/openms:3.2.0--haddbca4_4' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.3.0--h0656172_8':
+        'biocontainers/openms:3.3.0--h0656172_8' }"
 
     input:
     tuple val(meta), path(merged_idxml)
diff --git a/modules/nf-core/openms/idripper/tests/main.nf.test.snap b/modules/nf-core/openms/idripper/tests/main.nf.test.snap
index 2851a262ca8..3e1b2d76ca3 100644
--- a/modules/nf-core/openms/idripper/tests/main.nf.test.snap
+++ b/modules/nf-core/openms/idripper/tests/main.nf.test.snap
@@ -14,7 +14,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e016c1da0449e1d29d4c34198ff1a948"
+                    "versions.yml:md5,6bb62c7c19af0216ac52a3a446d8f902"
                 ],
                 "idxmls": [
                     [
@@ -28,15 +28,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,e016c1da0449e1d29d4c34198ff1a948"
+                    "versions.yml:md5,6bb62c7c19af0216ac52a3a446d8f902"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-08T12:02:51.318615048"
+        "timestamp": "2025-01-27T09:57:07.224001216"
     },
     "proteomics - split - idxml - stub": {
         "content": [
@@ -53,7 +53,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e016c1da0449e1d29d4c34198ff1a948"
+                    "versions.yml:md5,6bb62c7c19af0216ac52a3a446d8f902"
                 ],
                 "idxmls": [
                     [
@@ -67,14 +67,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,e016c1da0449e1d29d4c34198ff1a948"
+                    "versions.yml:md5,6bb62c7c19af0216ac52a3a446d8f902"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-08T12:02:59.481185212"
+        "timestamp": "2025-01-27T09:57:16.528990416"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/openms/idscoreswitcher/environment.yml b/modules/nf-core/openms/idscoreswitcher/environment.yml
index 5ec74436391..6c42dcb14bc 100644
--- a/modules/nf-core/openms/idscoreswitcher/environment.yml
+++ b/modules/nf-core/openms/idscoreswitcher/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::openms=3.2.0"
+  - "bioconda::openms=3.3.0"
diff --git a/modules/nf-core/openms/idscoreswitcher/main.nf b/modules/nf-core/openms/idscoreswitcher/main.nf
index 41ecb2df7fb..0f4e4e5246f 100644
--- a/modules/nf-core/openms/idscoreswitcher/main.nf
+++ b/modules/nf-core/openms/idscoreswitcher/main.nf
@@ -4,8 +4,8 @@ process OPENMS_IDSCORESWITCHER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4':
-        'biocontainers/openms:3.2.0--haddbca4_4' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.3.0--h0656172_8':
+        'biocontainers/openms:3.3.0--h0656172_8' }"
 
     input:
     tuple val(meta), path(idxml)
diff --git a/modules/nf-core/openms/idscoreswitcher/tests/main.nf.test.snap b/modules/nf-core/openms/idscoreswitcher/tests/main.nf.test.snap
index 287209db145..d235a3c58c4 100644
--- a/modules/nf-core/openms/idscoreswitcher/tests/main.nf.test.snap
+++ b/modules/nf-core/openms/idscoreswitcher/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,6ba0a7c237c0553ecaa343d7d0638e32"
+                    "versions.yml:md5,cbfb6033f465c5cec51648340d64d4be"
                 ],
                 "idxml": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6ba0a7c237c0553ecaa343d7d0638e32"
+                    "versions.yml:md5,cbfb6033f465c5cec51648340d64d4be"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-08T12:08:26.611231415"
+        "timestamp": "2025-01-27T09:57:29.949315209"
     },
     "proteomics - switch_score - idxml": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,6ba0a7c237c0553ecaa343d7d0638e32"
+                    "versions.yml:md5,cbfb6033f465c5cec51648340d64d4be"
                 ],
                 "idxml": [
                     [
@@ -55,14 +55,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6ba0a7c237c0553ecaa343d7d0638e32"
+                    "versions.yml:md5,cbfb6033f465c5cec51648340d64d4be"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-08T12:08:17.9635299"
+        "timestamp": "2025-01-27T09:57:23.221927789"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/openms/peakpickerhires/environment.yml b/modules/nf-core/openms/peakpickerhires/environment.yml
index d4d40e896b1..6c42dcb14bc 100644
--- a/modules/nf-core/openms/peakpickerhires/environment.yml
+++ b/modules/nf-core/openms/peakpickerhires/environment.yml
@@ -1,7 +1,5 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::openms=3.2.0"
+  - "bioconda::openms=3.3.0"
diff --git a/modules/nf-core/openms/peakpickerhires/main.nf b/modules/nf-core/openms/peakpickerhires/main.nf
index 153cab4f91a..447fcc08298 100644
--- a/modules/nf-core/openms/peakpickerhires/main.nf
+++ b/modules/nf-core/openms/peakpickerhires/main.nf
@@ -4,8 +4,8 @@ process OPENMS_PEAKPICKERHIRES {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4' :
-        'biocontainers/openms:3.2.0--haddbca4_4' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.3.0--h0656172_8' :
+        'biocontainers/openms:3.3.0--h0656172_8' }"
 
     input:
     tuple val(meta), path(mzml)
diff --git a/modules/nf-core/openms/peakpickerhires/tests/main.nf.test.snap b/modules/nf-core/openms/peakpickerhires/tests/main.nf.test.snap
index c99a542ed53..ee83a13b342 100644
--- a/modules/nf-core/openms/peakpickerhires/tests/main.nf.test.snap
+++ b/modules/nf-core/openms/peakpickerhires/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "proteomics - mzML": {
         "content": [
             [
-                "versions.yml:md5,3db8a4b45ffebff2eac6118cbca4bb4e"
+                "versions.yml:md5,2a295ece38dbed69c3a865da59cbd36e"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-08T12:13:25.732124582"
+        "timestamp": "2025-01-27T09:57:37.304798738"
     },
     "proteomics - mzML - stub": {
         "content": [
@@ -23,7 +23,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,3db8a4b45ffebff2eac6118cbca4bb4e"
+                    "versions.yml:md5,2a295ece38dbed69c3a865da59cbd36e"
                 ],
                 "mzml": [
                     [
@@ -34,14 +34,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3db8a4b45ffebff2eac6118cbca4bb4e"
+                    "versions.yml:md5,2a295ece38dbed69c3a865da59cbd36e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-08T12:13:32.716358119"
+        "timestamp": "2025-01-27T09:57:44.129648263"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/openms/peptideindexer/environment.yml b/modules/nf-core/openms/peptideindexer/environment.yml
index d6e51812af3..db74dae3815 100644
--- a/modules/nf-core/openms/peptideindexer/environment.yml
+++ b/modules/nf-core/openms/peptideindexer/environment.yml
@@ -3,4 +3,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::openms=3.2.0"
+  - "bioconda::openms=3.3.0"
diff --git a/modules/nf-core/openms/peptideindexer/main.nf b/modules/nf-core/openms/peptideindexer/main.nf
index 2bf824c3931..18cb37bff3e 100644
--- a/modules/nf-core/openms/peptideindexer/main.nf
+++ b/modules/nf-core/openms/peptideindexer/main.nf
@@ -4,15 +4,14 @@ process OPENMS_PEPTIDEINDEXER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4':
-        'biocontainers/openms:3.2.0--haddbca4_4' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.3.0--h0656172_8' :
+        'biocontainers/openms:3.3.0--h0656172_8' }"
 
     input:
-    tuple val(meta), path(id_file)
-    tuple val(meta), path(id_fasta)
+    tuple val(meta), path(idxml), path(fasta)
 
     output:
-    tuple val(meta), path("*.idXML"), emit: id_file_pi
+    tuple val(meta), path("*.idXML"), emit: indexed_idxml
     path "versions.yml"             , emit: versions
 
     when:
@@ -20,15 +19,17 @@ process OPENMS_PEPTIDEINDEXER {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}_pi"
+    def prefix = task.ext.prefix ?: "${meta.id}_indexed"
+    def fasta_file = fasta ? "-fasta ${fasta}": ""
+
 
     """
     PeptideIndexer \\
-        -in $id_file \\
-        -fasta $id_fasta \\
+        -in $idxml \\
+        $fasta_file \\
         -out ${prefix}.idXML \\
         -threads $task.cpus \\
-        $args \\
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -38,7 +39,7 @@ process OPENMS_PEPTIDEINDEXER {
 
     stub:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}_pi"
+    def prefix = task.ext.prefix ?: "${meta.id}_indexed"
 
     """
     touch ${prefix}.idXML
diff --git a/modules/nf-core/openms/peptideindexer/meta.yml b/modules/nf-core/openms/peptideindexer/meta.yml
index 10f808d2385..c55a5927122 100644
--- a/modules/nf-core/openms/peptideindexer/meta.yml
+++ b/modules/nf-core/openms/peptideindexer/meta.yml
@@ -20,31 +20,26 @@ input:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. `[ id:'sample1', single_end:false ]`
-    - id_file:
+          e.g. `[ id:'sample1' ]`
+    - idxml:
         type: file
         description: idXML identification file
-        pattern: "*.{idXML}"
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. `[ id:'sample1', single_end:false ]`
-    - id_fasta:
+        pattern: "*.idXML"
+    - fasta:
         type: file
         description: Input sequence database in FASTA format
         pattern: "*.fasta"
 output:
-  - id_file_pi:
+  - indexed_idxml:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. `[ id:'sample1', single_end:false ]`
+            e.g. `[ id:'sample1' ]`
       - "*.idXML":
           type: file
           description: Refreshed idXML identification file
-          pattern: "*.{idXML}"
+          pattern: "*.idXML"
   - versions:
       - versions.yml:
           type: file
diff --git a/modules/nf-core/openms/peptideindexer/tests/main.nf.test b/modules/nf-core/openms/peptideindexer/tests/main.nf.test
index 1238bc361de..df8bded7cc5 100644
--- a/modules/nf-core/openms/peptideindexer/tests/main.nf.test
+++ b/modules/nf-core/openms/peptideindexer/tests/main.nf.test
@@ -3,13 +3,12 @@ nextflow_process {
     name "Test Process OPENMS_PEPTIDEINDEXER"
     script "../main.nf"
     process "OPENMS_PEPTIDEINDEXER"
-    config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
     tag "openms"
-    tag "openms/decoydatabase"
     tag "openms/peptideindexer"
+    tag "openms/decoydatabase"
 
     setup {
         run("OPENMS_DECOYDATABASE") {
@@ -18,24 +17,23 @@ nextflow_process {
                 """
                 input[0] = [
                     [id:'test'],
-                    file(params.modules_testdata_base_path + 'proteomics/database/UP000005640_9606.fasta', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'proteomics/database/yeast_UPS.fasta', checkIfExists: true)
                 ]
                 """
             }
         }
     }
 
-   test("proteomics - refresh_idxml") {
+    test("proteomics - refresh_idxml") {
 
         when {
             process {
                 """
                 input[0] = [
                     [id:'test'],
-                    file(params.modules_testdata_base_path + 'proteomics/openms/HepG2_rep1_small.idXML', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'proteomics/openms/HepG2_rep1_small.idXML', checkIfExists: true),
+                    OPENMS_DECOYDATABASE.out.decoy_fasta[0][1]
                 ]
-                input[1] = OPENMS_DECOYDATABASE.out.decoy_fasta
-
                 """
             }
         }
@@ -46,7 +44,6 @@ nextflow_process {
                 { assert snapshot(process.out).match() }
             )
         }
-
     }
 
     test("proteomics - refresh_idxml - stub") {
@@ -58,10 +55,9 @@ nextflow_process {
                 """
                 input[0] = [
                     [id:'test'],
-                    file(params.modules_testdata_base_path + 'proteomics/openms/HepG2_rep1_small.idXML', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'proteomics/openms/HepG2_rep1_small.idXML', checkIfExists: true),
+                    OPENMS_DECOYDATABASE.out.decoy_fasta[0][1]
                 ]
-                input[1] = OPENMS_DECOYDATABASE.out.decoy_fasta
-
                 """
             }
         }
@@ -72,7 +68,5 @@ nextflow_process {
                 { assert snapshot(process.out).match() }
             )
         }
-
     }
-
 }
diff --git a/modules/nf-core/openms/peptideindexer/tests/main.nf.test.snap b/modules/nf-core/openms/peptideindexer/tests/main.nf.test.snap
index bc41f96655e..bc283a3370a 100644
--- a/modules/nf-core/openms/peptideindexer/tests/main.nf.test.snap
+++ b/modules/nf-core/openms/peptideindexer/tests/main.nf.test.snap
@@ -3,34 +3,24 @@
         "content": [
             {
                 "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test_pi.idXML:md5,f18620bed99c99f292b4e1804c3a47ad"
-                    ]
+                    
                 ],
                 "1": [
-                    "versions.yml:md5,01ee06728114ec0a7b0980ad83eedd42"
+                    
                 ],
-                "id_file_pi": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test_pi.idXML:md5,f18620bed99c99f292b4e1804c3a47ad"
-                    ]
+                "indexed_idxml": [
+                    
                 ],
                 "versions": [
-                    "versions.yml:md5,01ee06728114ec0a7b0980ad83eedd42"
+                    
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-08T11:26:20.161342857"
+        "timestamp": "2025-01-28T10:38:52.253777904"
     },
     "proteomics - refresh_idxml - stub": {
         "content": [
@@ -40,29 +30,29 @@
                         {
                             "id": "test"
                         },
-                        "test_pi.idXML:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_indexed.idXML:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,01ee06728114ec0a7b0980ad83eedd42"
+                    "versions.yml:md5,b7c2ec6b3b6a287ffacfe1b91977bff0"
                 ],
-                "id_file_pi": [
+                "indexed_idxml": [
                     [
                         {
                             "id": "test"
                         },
-                        "test_pi.idXML:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_indexed.idXML:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,01ee06728114ec0a7b0980ad83eedd42"
+                    "versions.yml:md5,b7c2ec6b3b6a287ffacfe1b91977bff0"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-08T11:26:28.558838022"
+        "timestamp": "2025-01-28T15:08:52.058836152"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/openms/peptideindexer/tests/nextflow.config b/modules/nf-core/openms/peptideindexer/tests/nextflow.config
deleted file mode 100644
index 33c1adcd7a6..00000000000
--- a/modules/nf-core/openms/peptideindexer/tests/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
-    withName:OPENMS_PEPTIDEINDEXER {
-
-        ext.args = "-missing_decoy_action 'silent' -unmatched_action 'remove'"
-
-        }
-
-}
diff --git a/modules/nf-core/openmsthirdparty/cometadapter/environment.yml b/modules/nf-core/openmsthirdparty/cometadapter/environment.yml
index dfc10603608..2e67e21bb8c 100644
--- a/modules/nf-core/openmsthirdparty/cometadapter/environment.yml
+++ b/modules/nf-core/openmsthirdparty/cometadapter/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::openms-thirdparty=3.2.0"
+  - "bioconda::openms-thirdparty=3.3.0"
diff --git a/modules/nf-core/openmsthirdparty/cometadapter/main.nf b/modules/nf-core/openmsthirdparty/cometadapter/main.nf
index 15a28391d56..c75735f5608 100644
--- a/modules/nf-core/openmsthirdparty/cometadapter/main.nf
+++ b/modules/nf-core/openmsthirdparty/cometadapter/main.nf
@@ -4,8 +4,8 @@ process OPENMSTHIRDPARTY_COMETADAPTER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.2.0--h9ee0642_4' :
-        'biocontainers/openms-thirdparty:3.2.0--h9ee0642_4' }"
+        'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
+        'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"
 
     input:
     tuple val(meta), path(mzml), path(fasta)
diff --git a/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test.snap b/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test.snap
index 939aa4151ec..d95fcfb946e 100644
--- a/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test.snap
+++ b/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test.snap
@@ -45,15 +45,15 @@
         "content": [
             {
                 "OPENMSTHIRDPARTY_COMETADAPTER": {
-                    "CometAdapter": "3.2.0",
+                    "CometAdapter": "3.3.0",
                     "Comet": "2023.01 rev. 2"
                 }
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-10-08T11:29:53.094774827"
+        "timestamp": "2025-01-27T09:42:28.84181934"
     }
 }
\ No newline at end of file