nf-core · SPPearce · Nov 1, 2025 · Nov 1, 2025 · Nov 1, 2025 · Nov 1, 2025
diff --git a/modules/nf-core/metaeuk/easypredict/tests/main.nf.test b/modules/nf-core/metaeuk/easypredict/tests/main.nf.test
@@ -41,7 +41,7 @@ nextflow_process {
 
                 process {
                     """
-                    input[0] = 'UniProtKB/Swiss-Prot'
+                    input[0] = 'Kalamari'
                     """
                 }
             }

diff --git a/modules/nf-core/metaeuk/easypredict/tests/main.nf.test.snap b/modules/nf-core/metaeuk/easypredict/tests/main.nf.test.snap
@@ -174,31 +174,31 @@
                         {
                             "id": "test"
                         },
-                        "test.fas:md5,3834a7d4dc4f7da755afc00b73589a1b"
+                        "test.fas:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.codon.fas:md5,21e47f601e73834f96a61f5150535716"
+                        "test.codon.fas:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "2": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.headersMap.tsv:md5,518ed985e5dad185ba2e8228c540c059"
+                        "test.headersMap.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "3": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.gff:md5,0d1e318931bb2b441fbc035137b7fc49"
+                        "test.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "4": [
@@ -209,31 +209,31 @@
                         {
                             "id": "test"
                         },
-                        "test.codon.fas:md5,21e47f601e73834f96a61f5150535716"
+                        "test.codon.fas:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "faa": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.fas:md5,3834a7d4dc4f7da755afc00b73589a1b"
+                        "test.fas:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "gff": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.gff:md5,0d1e318931bb2b441fbc035137b7fc49"
+                        "test.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "tsv": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.headersMap.tsv:md5,518ed985e5dad185ba2e8228c540c059"
+                        "test.headersMap.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
@@ -243,8 +243,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-25T08:18:53.256041749"
+        "timestamp": "2025-11-01T17:50:24.868686992"
     }
 }
diff --git a/modules/nf-core/mmseqs/cluster/environment.yml b/modules/nf-core/mmseqs/cluster/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::mmseqs2=17.b804f
+  - bioconda::mmseqs2=18.8cc5c
diff --git a/modules/nf-core/mmseqs/cluster/main.nf b/modules/nf-core/mmseqs/cluster/main.nf
@@ -1,18 +1,18 @@
 process MMSEQS_CLUSTER {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1':
-        'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fe/fe49c17754753d6cd9a31e5894117edaf1c81e3d6053a12bf6dc8f3af1dffe23/data'
+        : 'community.wave.seqera.io/library/mmseqs2:18.8cc5c--af05c9a98d9f6139'}"
 
     input:
     tuple val(meta), path(db_input)
 
     output:
     tuple val(meta), path("${prefix}/"), emit: db_cluster
-    path "versions.yml"                , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,19 +21,21 @@ process MMSEQS_CLUSTER {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: "*.dbtype"
     prefix = task.ext.prefix ?: "${meta.id}"
-    if ("$db_input" == "${prefix}") error "Input and output names of databases are the same, set prefix in module configuration to disambiguate!"
+    if ("${db_input}" == "${prefix}") {
+        error("Input and output names of databases are the same, set prefix in module configuration to disambiguate!")
+    }
 
     """
     mkdir -p ${prefix}
     # Extract files with specified args based suffix | remove suffix | isolate longest common substring of files
-    DB_INPUT_PATH_NAME=\$(find -L "$db_input/" -maxdepth 1 -name "$args2" | sed 's/\\.[^.]*\$//' |  sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' )
+    DB_INPUT_PATH_NAME=\$(find -L "${db_input}/" -maxdepth 1 -name "${args2}" | sed 's/\\.[^.]*\$//' |  sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' )
 
     mmseqs \\
         cluster \\
         \$DB_INPUT_PATH_NAME \\
         ${prefix}/${prefix} \\
         tmp1 \\
-        $args \\
+        ${args} \\
         --threads ${task.cpus}
 
     cat <<-END_VERSIONS > versions.yml
@@ -46,6 +48,7 @@ process MMSEQS_CLUSTER {
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     """
+    echo ${args}
     mkdir -p ${prefix}
 
     touch ${prefix}/${prefix}.{0..9}

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:md5,8cd8fdc3e9d128b0a4dc634b8748c213"
+            "versions.yml:md5,b53987961652676f677105ea360a633f"
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-01-20T14:07:52.454357"
+        "timestamp": "2025-11-01T16:18:22.334709172"
     }
 }
diff --git a/modules/nf-core/mmseqs/createdb/environment.yml b/modules/nf-core/mmseqs/createdb/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::mmseqs2=17.b804f
+  - bioconda::mmseqs2=18.8cc5c
diff --git a/modules/nf-core/mmseqs/createdb/main.nf b/modules/nf-core/mmseqs/createdb/main.nf
@@ -1,18 +1,18 @@
 process MMSEQS_CREATEDB {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1':
-        'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fe/fe49c17754753d6cd9a31e5894117edaf1c81e3d6053a12bf6dc8f3af1dffe23/data'
+        : 'community.wave.seqera.io/library/mmseqs2:18.8cc5c--af05c9a98d9f6139'}"
 
     input:
     tuple val(meta), path(sequence)
 
     output:
     tuple val(meta), path("${prefix}/"), emit: db
-    path "versions.yml"                , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -33,7 +33,7 @@ process MMSEQS_CREATEDB {
         createdb \\
         ${sequence_name} \\
         ${prefix}/${prefix} \\
-        $args
+        ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -45,6 +45,7 @@ process MMSEQS_CREATEDB {
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     """
+    echo ${args}
     mkdir -p ${prefix}
 
     touch ${prefix}/${prefix}

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,c62b08152082097334109fe08ec6333a"
+                "versions.yml:md5,02a6806d10988baae0ab644d671f113c"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-01-20T14:11:57.883871"
+        "timestamp": "2025-11-01T16:18:26.983758708"
     },
     "Should build an mmseqs db from a zipped amino acid sequence file": {
         "content": [
@@ -49,13 +49,13 @@
                 ]
             ],
             [
-                "versions.yml:md5,c62b08152082097334109fe08ec6333a"
+                "versions.yml:md5,02a6806d10988baae0ab644d671f113c"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-01-20T14:12:10.986433"
+        "timestamp": "2025-11-01T16:18:31.492266142"
     }
 }
diff --git a/modules/nf-core/mmseqs/createindex/environment.yml b/modules/nf-core/mmseqs/createindex/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::mmseqs2=17.b804f
+  - bioconda::mmseqs2=18.8cc5c
diff --git a/modules/nf-core/mmseqs/createindex/main.nf b/modules/nf-core/mmseqs/createindex/main.nf
@@ -5,8 +5,8 @@ process MMSEQS_CREATEINDEX {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/mmseqs2:17.b804f--hd6d6fdc_1'
-        : 'biocontainers/mmseqs2:17.b804f--hd6d6fdc_1'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fe/fe49c17754753d6cd9a31e5894117edaf1c81e3d6053a12bf6dc8f3af1dffe23/data'
+        : 'community.wave.seqera.io/library/mmseqs2:18.8cc5c--af05c9a98d9f6139'}"
 
     input:
     tuple val(meta), path(db)
@@ -21,8 +21,6 @@ process MMSEQS_CREATEINDEX {
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: "*.dbtype"
-    def prefix = task.ext.prefix ?: "${meta.id}"
-
     """
     DB_INPUT_PATH_NAME=\$(find -L "${db}/" -maxdepth 1 -name "${args2}" | sed 's/\\.[^.]*\$//' |  sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' )
 
@@ -45,7 +43,7 @@ process MMSEQS_CREATEINDEX {
     """
     DB_INPUT_PATH_NAME=\$(find -L "${db}/" -maxdepth 1 -name "${args2}" | sed 's/\\.[^.]*\$//' |  sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' )
 
-    touch "\${DB_PATH_NAME}.idx"
+    touch "\${DB_INPUT_PATH_NAME}.idx"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

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:md5,9745ec52ea0356d97ef2f5c18c01d7e7"
+                "versions.yml:md5,35132b6bcef6fb9a674a5f346c57282d"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-01-20T17:15:56.23597"
+        "timestamp": "2025-11-01T16:18:37.261481775"
     },
     "createindex_filtered_files": {
         "content": [
@@ -18,7 +18,7 @@
                 "mmseqs.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
                 "mmseqs.fasta:md5,b40600ad3be77f076df716e6cf99c64c",
                 "mmseqs.idx.dbtype:md5,9a198d4f48144e20661df7fd2dc41bf7",
-                "mmseqs.idx.index:md5,7c1dc5d8044ab7e0535d0ba4d7b7ab07",
+                "mmseqs.idx.index:md5,3451d87bd8a5a7182d36d53edd213c59",
                 "mmseqs.index:md5,c012bdab1c61eeafcb99d1b26650f3d0",
                 "mmseqs.lookup:md5,fa898551a6b303614ae6e29c237b7fc6",
                 "mmseqs.source:md5,16bef02c30aadbfa8d035596502f0aa2",
@@ -55,8 +55,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-01-20T17:15:56.186115"
+        "timestamp": "2025-11-01T16:18:37.253778342"
     }
 }
diff --git a/modules/nf-core/mmseqs/createtsv/environment.yml b/modules/nf-core/mmseqs/createtsv/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::mmseqs2=17.b804f
+  - bioconda::mmseqs2=18.8cc5c
-Original file line number
+Diff line change
@@ Expand Up / @@ -41,7 +41,7 @@ nextflow_process { @@
                     process {
                         """
-                        input[0] = 'UniProtKB/Swiss-Prot'
+                        input[0] = 'Kalamari'
                         """
                     }
                 }
@@ Expand Down @@