Bump openms tools to version 3.2.0 (#6754)

* update container version-tag * update snapshots * bump conda versions
nf-core · Oct 11, 2024 · 573ba82 · 573ba82
1 parent cf17ca4
commit 573ba82
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Showing 28 changed files with 118 additions and 102 deletions.
diff --git 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=3.1.0
+  - bioconda::openms=3.2.0
diff --git 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:3.1.0--h8964181_3' :
-        'biocontainers/openms:3.1.0--h8964181_3' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4' :
+        'biocontainers/openms:3.2.0--haddbca4_4' }"
 
     input:
     tuple val(meta), path(fasta)

diff --git 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:md5,29955625bab2d7680a741faab680f3a6"
+                    "versions.yml:md5,6c32e4ec0949f616baefa1b17efbe426"
                 ],
                 "decoy_fasta": [
                     [
@@ -22,14 +22,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,29955625bab2d7680a741faab680f3a6"
+                    "versions.yml:md5,6c32e4ec0949f616baefa1b17efbe426"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-12T16:26:35.886966049"
+        "timestamp": "2024-10-08T11:22:32.701406062"
     }
 }
diff --git 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=3.1.0"
+  - "bioconda::openms=3.2.0"
diff --git 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=3.1.0"
+    conda "bioconda::openms=3.2.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.1.0--h8964181_3' :
-        'biocontainers/openms:3.1.0--h8964181_3' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4' :
+        'biocontainers/openms:3.2.0--haddbca4_4' }"
 
     input:
     tuple val(meta), path(id_file), path(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
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,180b8b0b5aa3a0439c4695e8c2a20c7b"
+                    "versions.yml:md5,8a95c69294e90ae931b766218dc87dec"
                 ],
                 "filtered": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,180b8b0b5aa3a0439c4695e8c2a20c7b"
+                    "versions.yml:md5,8a95c69294e90ae931b766218dc87dec"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-18T12:24:23.590979361"
+        "timestamp": "2024-10-08T11:45:00.758602574"
     },
     "proteomics - filter - idxml": {
         "content": [
@@ -40,29 +40,29 @@
                         {
                             "id": "test"
                         },
-                        "test.idXML:md5,9efbb130c9a34807a4db1be64a7d395f"
+                        "test.idXML:md5,59b0c4592ee45e1d2158b399ba838002"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,180b8b0b5aa3a0439c4695e8c2a20c7b"
+                    "versions.yml:md5,8a95c69294e90ae931b766218dc87dec"
                 ],
                 "filtered": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.idXML:md5,9efbb130c9a34807a4db1be64a7d395f"
+                        "test.idXML:md5,59b0c4592ee45e1d2158b399ba838002"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,180b8b0b5aa3a0439c4695e8c2a20c7b"
+                    "versions.yml:md5,8a95c69294e90ae931b766218dc87dec"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-18T12:24:09.504917196"
+        "timestamp": "2024-10-08T11:44:53.291545021"
     }
 }
diff --git 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=3.1.0"
+  - "bioconda::openms=3.2.0"
diff --git 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:3.1.0--h191ead1_4' :
-        'biocontainers/openms:3.1.0--h191ead1_4' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4' :
+        'biocontainers/openms:3.2.0--haddbca4_4' }"
 
     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
@@ -19,7 +19,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,84212cbbf016bbcae0eb1bb0fcc30db7"
+                    "versions.yml:md5,9bf83a6db02732d209de6819818aed26"
                 ],
                 "frag_err": [
                     [
@@ -38,15 +38,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,84212cbbf016bbcae0eb1bb0fcc30db7"
+                    "versions.yml:md5,9bf83a6db02732d209de6819818aed26"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-16T05:12:06.655389198"
+        "timestamp": "2024-10-08T11:26:08.231171982"
     },
     "proteomics - openms - mass_error": {
         "content": [
@@ -63,7 +63,7 @@
 
                 ],
                 "2": [
-                    "versions.yml:md5,84212cbbf016bbcae0eb1bb0fcc30db7"
+                    "versions.yml:md5,9bf83a6db02732d209de6819818aed26"
                 ],
                 "frag_err": [
                     [
@@ -77,14 +77,14 @@
 
                 ],
                 "versions": [
-                    "versions.yml:md5,84212cbbf016bbcae0eb1bb0fcc30db7"
+                    "versions.yml:md5,9bf83a6db02732d209de6819818aed26"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-16T05:11:55.087464408"
+        "timestamp": "2024-10-08T11:25:57.38948188"
     }
 }
diff --git 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=3.1.0
+  - bioconda::openms=3.2.0
diff --git 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:3.1.0--h8964181_3' :
-        'biocontainers/openms:3.1.0--h8964181_3' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4' :
+        'biocontainers/openms:3.2.0--haddbca4_4' }"
 
     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
@@ -2,14 +2,14 @@
     "proteomics - openms - idxml": {
         "content": [
             [
-                "versions.yml:md5,09d83e713284f55e18cebcc20eda07b9"
+                "versions.yml:md5,8051ce1c0fe4404798507d607ebf52a3"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-12T17:33:25.047982404"
+        "timestamp": "2024-10-08T12:02:35.595648853"
     },
     "proteomics - openms - idxml - stub": {
         "content": [
@@ -23,7 +23,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,09d83e713284f55e18cebcc20eda07b9"
+                    "versions.yml:md5,8051ce1c0fe4404798507d607ebf52a3"
                 ],
                 "idxml": [
                     [
@@ -34,14 +34,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,09d83e713284f55e18cebcc20eda07b9"
+                    "versions.yml:md5,8051ce1c0fe4404798507d607ebf52a3"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-12T17:33:34.498327729"
+        "timestamp": "2024-10-08T12:02:42.76246364"
     }
 }
diff --git 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=3.1.0"
+  - "bioconda::openms=3.2.0"
diff --git 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:3.1.0--h8964181_3':
-        'biocontainers/openms:3.1.0--h8964181_3' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4':
+        'biocontainers/openms:3.2.0--haddbca4_4' }"
 
     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
@@ -8,31 +8,35 @@
                             "id": "test"
                         },
                         [
-                            "HepG2_rep1_small.idXML:md5,ca1c4549a42e0b0c0be8345cf5062dfd",
-                            "HepG2_rep2_small.idXML:md5,14a4e9a7dca3c62db38b6345a63d80d5"
+                            "HepG2_rep1_small.idXML:md5,0124479eaf5bba215a801aff613f08d6",
+                            "HepG2_rep2_small.idXML:md5,4b26909ad111957d4bbfa9981c80e92d"
                         ]
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,7a7ebf177e4987780b6371dab640e6c0"
+                    "versions.yml:md5,e016c1da0449e1d29d4c34198ff1a948"
                 ],
                 "idxmls": [
                     [
                         {
                             "id": "test"
                         },
                         [
-                            "HepG2_rep1_small.idXML:md5,ca1c4549a42e0b0c0be8345cf5062dfd",
-                            "HepG2_rep2_small.idXML:md5,14a4e9a7dca3c62db38b6345a63d80d5"
+                            "HepG2_rep1_small.idXML:md5,0124479eaf5bba215a801aff613f08d6",
+                            "HepG2_rep2_small.idXML:md5,4b26909ad111957d4bbfa9981c80e92d"
                         ]
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,7a7ebf177e4987780b6371dab640e6c0"
+                    "versions.yml:md5,e016c1da0449e1d29d4c34198ff1a948"
                 ]
             }
         ],
-        "timestamp": "2024-01-05T10:53:57.761966016"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-08T12:02:51.318615048"
     },
     "proteomics - split - idxml - stub": {
         "content": [
@@ -49,7 +53,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,7a7ebf177e4987780b6371dab640e6c0"
+                    "versions.yml:md5,e016c1da0449e1d29d4c34198ff1a948"
                 ],
                 "idxmls": [
                     [
@@ -63,10 +67,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,7a7ebf177e4987780b6371dab640e6c0"
+                    "versions.yml:md5,e016c1da0449e1d29d4c34198ff1a948"
                 ]
             }
         ],
-        "timestamp": "2024-01-05T10:54:05.672792514"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-08T12:02:59.481185212"
     }
 }
diff --git 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=3.1.0"
+  - "bioconda::openms=3.2.0"
diff --git 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:3.1.0--h8964181_3':
-        'biocontainers/openms:3.1.0--h8964181_3' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4':
+        'biocontainers/openms:3.2.0--haddbca4_4' }"
 
     input:
     tuple val(meta), path(idxml)