nf-core · jfy133 · Jan 21, 2025 · Jan 20, 2025
diff --git a/modules/nf-core/mmseqs/cluster/environment.yml b/modules/nf-core/mmseqs/cluster/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::mmseqs2=16.747c6
+  - bioconda::mmseqs2=17.b804f
diff --git a/modules/nf-core/mmseqs/cluster/main.nf b/modules/nf-core/mmseqs/cluster/main.nf
@@ -4,8 +4,8 @@ process MMSEQS_CLUSTER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0':
-        'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }"
+        'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1':
+        'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1' }"
 
     input:
     tuple val(meta), path(db_input)

diff --git a/modules/nf-core/mmseqs/cluster/tests/main.nf.test.snap b/modules/nf-core/mmseqs/cluster/tests/main.nf.test.snap
@@ -11,12 +11,12 @@
                 "test_output_cluster.dbtype:md5,b9d9c6dbc098c97ae446f612efd8eafd",
                 "test_output_cluster.index:md5,9848b52b6df827d80a04f7c71c50056b"
             ],
-            "versions.yml:md5,4acad55952c6d1fb41ad7f5a44468aed"
+            "versions.yml:md5,8cd8fdc3e9d128b0a4dc634b8748c213"
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-15T19:30:14.704271821"
+        "timestamp": "2025-01-20T14:07:52.454357"
     }
 }
diff --git a/modules/nf-core/mmseqs/createdb/environment.yml b/modules/nf-core/mmseqs/createdb/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::mmseqs2=16.747c6
+  - bioconda::mmseqs2=17.b804f
diff --git a/modules/nf-core/mmseqs/createdb/main.nf b/modules/nf-core/mmseqs/createdb/main.nf
@@ -4,8 +4,8 @@ process MMSEQS_CREATEDB {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0':
-        'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }"
+        'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1':
+        'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1' }"
 
     input:
     tuple val(meta), path(sequence)

diff --git a/modules/nf-core/mmseqs/createdb/tests/main.nf.test.snap b/modules/nf-core/mmseqs/createdb/tests/main.nf.test.snap
@@ -20,14 +20,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,d30a1af41e7f3f5b67afdec412fa693f"
+                "versions.yml:md5,c62b08152082097334109fe08ec6333a"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-15T19:30:25.339409238"
+        "timestamp": "2025-01-20T14:11:57.883871"
     },
     "Should build an mmseqs db from a zipped amino acid sequence file": {
         "content": [
@@ -49,13 +49,13 @@
                 ]
             ],
             [
-                "versions.yml:md5,d30a1af41e7f3f5b67afdec412fa693f"
+                "versions.yml:md5,c62b08152082097334109fe08ec6333a"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-15T19:30:34.93361715"
+        "timestamp": "2025-01-20T14:12:10.986433"
     }
 }
diff --git a/modules/nf-core/mmseqs/createindex/environment.yml b/modules/nf-core/mmseqs/createindex/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::mmseqs2=16.747c6
+  - bioconda::mmseqs2=17.b804f
diff --git a/modules/nf-core/mmseqs/createindex/main.nf b/modules/nf-core/mmseqs/createindex/main.nf
@@ -4,8 +4,8 @@ process MMSEQS_CREATEINDEX {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0'
-        : 'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0'}"
+        ? 'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1'
+        : 'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1'}"
 
     input:
     tuple val(meta), path(db)

diff --git a/modules/nf-core/mmseqs/createindex/tests/main.nf.test.snap b/modules/nf-core/mmseqs/createindex/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "versions": {
         "content": [
             [
-                "versions.yml:md5,227ad351b62984329aabf90242522eee"
+                "versions.yml:md5,9745ec52ea0356d97ef2f5c18c01d7e7"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-16T13:17:27.724764877"
+        "timestamp": "2025-01-20T17:15:56.23597"
     },
     "createindex_filtered_files": {
         "content": [
@@ -18,7 +18,7 @@
                 "mmseqs.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
                 "mmseqs.fasta:md5,b40600ad3be77f076df716e6cf99c64c",
                 "mmseqs.idx.dbtype:md5,9a198d4f48144e20661df7fd2dc41bf7",
-                "mmseqs.idx.index:md5,deac42b3a049a1c8a251d81b6b9538c9",
+                "mmseqs.idx.index:md5,7c1dc5d8044ab7e0535d0ba4d7b7ab07",
                 "mmseqs.index:md5,c012bdab1c61eeafcb99d1b26650f3d0",
                 "mmseqs.lookup:md5,fa898551a6b303614ae6e29c237b7fc6",
                 "mmseqs.source:md5,16bef02c30aadbfa8d035596502f0aa2",
@@ -54,9 +54,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-07-09T10:43:46.077636"
+        "timestamp": "2025-01-20T17:15:56.186115"
     }
 }
diff --git a/modules/nf-core/mmseqs/createtsv/environment.yml b/modules/nf-core/mmseqs/createtsv/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::mmseqs2=16.747c6
+  - bioconda::mmseqs2=17.b804f
diff --git a/modules/nf-core/mmseqs/createtsv/main.nf b/modules/nf-core/mmseqs/createtsv/main.nf
@@ -5,8 +5,8 @@ process MMSEQS_CREATETSV {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0':
-        'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }"
+        'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1':
+        'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1' }"
 
     input:
     tuple val(meta), path(db_result)

diff --git a/modules/nf-core/mmseqs/createtsv/tests/main.nf.test.snap b/modules/nf-core/mmseqs/createtsv/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7"
+                    "versions.yml:md5,ce808eb9a57e201a48afec56168f9e77"
                 ],
                 "tsv": [
                     [
@@ -24,15 +24,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7"
+                    "versions.yml:md5,ce808eb9a57e201a48afec56168f9e77"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-05T10:50:48.386202112"
+        "timestamp": "2025-01-20T17:29:15.220926"
     },
     "mmseqs/createtsv - sarscov2 - cluster - stub": {
         "content": [
@@ -47,7 +47,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7"
+                    "versions.yml:md5,ce808eb9a57e201a48afec56168f9e77"
                 ],
                 "tsv": [
                     [
@@ -59,38 +59,50 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7"
+                    "versions.yml:md5,ce808eb9a57e201a48afec56168f9e77"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-05T10:50:56.33475153"
+        "timestamp": "2025-01-20T17:29:32.089204"
     },
     "mmseqs/createtsv - bacteroides_fragilis - taxonomy": {
         "content": [
             {
                 "0": [
-
+                    [
+                        {
+                            "id": "test_query",
+                            "single_end": false
+                        },
+                        "test_query.tsv:md5,9179f5c85b8b87a4dc998c9d17840161"
+                    ]
                 ],
                 "1": [
-
+                    "versions.yml:md5,ce808eb9a57e201a48afec56168f9e77"
                 ],
                 "tsv": [
-
+                    [
+                        {
+                            "id": "test_query",
+                            "single_end": false
+                        },
+                        "test_query.tsv:md5,9179f5c85b8b87a4dc998c9d17840161"
+                    ]
                 ],
                 "versions": [
-
+                    "versions.yml:md5,ce808eb9a57e201a48afec56168f9e77"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-16T14:29:41.214561285"
+        "timestamp": "2025-01-20T17:28:41.472818"
     },
     "mmseqs/createtsv - sarscov2 - cluster": {
         "content": [
@@ -105,7 +117,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7"
+                    "versions.yml:md5,ce808eb9a57e201a48afec56168f9e77"
                 ],
                 "tsv": [
                     [
@@ -117,14 +129,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,34bac3809a7eaf833a944be6888f83a7"
+                    "versions.yml:md5,ce808eb9a57e201a48afec56168f9e77"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-15T11:17:04.119521629"
+        "timestamp": "2025-01-20T17:28:58.633976"
     }
 }
diff --git a/modules/nf-core/mmseqs/databases/environment.yml b/modules/nf-core/mmseqs/databases/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::mmseqs2=16.747c6
+  - bioconda::mmseqs2=17.b804f
diff --git a/modules/nf-core/mmseqs/databases/main.nf b/modules/nf-core/mmseqs/databases/main.nf
@@ -4,8 +4,8 @@ process MMSEQS_DATABASES {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0':
-        'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }"
+        'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1':
+        'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1' }"
 
     input:
     val database

diff --git a/modules/nf-core/mmseqs/databases/tests/main.nf.test.snap b/modules/nf-core/mmseqs/databases/tests/main.nf.test.snap
@@ -15,14 +15,14 @@
                 "database_taxonomy"
             ],
             [
-                "versions.yml:md5,e236ec16fdc9f054d0a660d02e680255"
+                "versions.yml:md5,387bbb2d1d6bac273e8158743af4c856"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-05T14:33:16.697954954"
+        "timestamp": "2025-01-20T15:32:42.284982"
     },
     "test-mmseqs-databases-stub": {
         "content": [

diff --git a/modules/nf-core/mmseqs/easysearch/environment.yml b/modules/nf-core/mmseqs/easysearch/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::mmseqs2=16.747c6
+  - bioconda::mmseqs2=17.b804f
diff --git a/modules/nf-core/mmseqs/easysearch/main.nf b/modules/nf-core/mmseqs/easysearch/main.nf
@@ -4,8 +4,8 @@ process MMSEQS_EASYSEARCH {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0'
-        : 'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0'}"
+        ? 'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1'
+        : 'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1'}"
 
     input:
     tuple val(meta), path(fasta)

diff --git a/modules/nf-core/mmseqs/easysearch/tests/main.nf.test.snap b/modules/nf-core/mmseqs/easysearch/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,2486965fbe4dca06ebf5bc84782dec83"
+                    "versions.yml:md5,0459b89b5e5e838b3d5ee718443e08da"
                 ],
                 "tsv": [
                     [
@@ -24,15 +24,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2486965fbe4dca06ebf5bc84782dec83"
+                    "versions.yml:md5,0459b89b5e5e838b3d5ee718443e08da"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-16T14:14:22.925002111"
+        "timestamp": "2025-01-20T18:11:14.000659"
     },
     "sarscov2 - illumina - contigs - fasta - stub": {
         "content": [

diff --git a/modules/nf-core/mmseqs/linclust/environment.yml b/modules/nf-core/mmseqs/linclust/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::mmseqs2=16.747c6
+  - bioconda::mmseqs2=17.b804f
diff --git a/modules/nf-core/mmseqs/linclust/main.nf b/modules/nf-core/mmseqs/linclust/main.nf
@@ -4,8 +4,8 @@ process MMSEQS_LINCLUST {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mmseqs2:16.747c6--pl5321h6a68c12_0':
-        'biocontainers/mmseqs2:16.747c6--pl5321h6a68c12_0' }"
+        'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1':
+        'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1' }"
 
     input:
     tuple val(meta), path(db_input)

diff --git a/modules/nf-core/mmseqs/linclust/tests/main.nf.test.snap b/modules/nf-core/mmseqs/linclust/tests/main.nf.test.snap
@@ -11,12 +11,12 @@
                 "test_output_cluster.dbtype:md5,b9d9c6dbc098c97ae446f612efd8eafd",
                 "test_output_cluster.index:md5,a0b78f31aee2c327d72f32919814baf1"
             ],
-            "versions.yml:md5,969cb26241f66ac758c104f9561860b1"
+            "versions.yml:md5,acd9806d081cf15f08f26263bd9dfe80"
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-15T19:38:00.258247122"
+        "timestamp": "2025-01-20T18:13:05.966684"
     }
 }