nf-core · SPPearce · Aug 3, 2026
diff --git a/modules/nf-core/repeatmodeler/builddatabase/main.nf b/modules/nf-core/repeatmodeler/builddatabase/main.nf
@@ -12,7 +12,7 @@ process REPEATMODELER_BUILDDATABASE {
 
     output:
     tuple val(meta), path("${prefix}.*")    , emit: db
-    path "versions.yml"                     , emit: versions
+    tuple val("${task.process}"), val('repeatmodeler'), eval("RepeatModeler --version  2>&1 | sed 's/RepeatModeler version //'") , emit: versions_repeatmodeler, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,13 +21,8 @@ process REPEATMODELER_BUILDDATABASE {
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     BuildDatabase \\
-        -name $prefix \\
-        $fasta
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        repeatmodeler: \$(RepeatModeler --version | sed 's/RepeatModeler version //')
-    END_VERSIONS
+        -name ${prefix} \\
+        ${fasta}
     """
 
     stub:
@@ -41,10 +36,5 @@ process REPEATMODELER_BUILDDATABASE {
     touch ${prefix}.nog
     touch ${prefix}.nsq
     touch ${prefix}.translation
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        repeatmodeler: \$(RepeatModeler --version | sed 's/RepeatModeler version //')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/repeatmodeler/builddatabase/meta.yml b/modules/nf-core/repeatmodeler/builddatabase/meta.yml
@@ -1,4 +1,3 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "repeatmodeler_builddatabase"
 description: Create a database for RepeatModeler
 keywords:
@@ -7,12 +6,12 @@ keywords:
   - repeat
 tools:
   - "repeatmodeler":
-      description: "RepeatModeler is a de-novo repeat family identification and modeling
-        package."
+      description: "RepeatModeler is a de-novo repeat family identification and modeling package."
       homepage: "https://github.com/Dfam-consortium/RepeatModeler"
       documentation: "https://github.com/Dfam-consortium/RepeatModeler"
       tool_dev_url: "https://github.com/Dfam-consortium/RepeatModeler"
-      licence: ["Open Software License v2.1"]
+      licence:
+        - "Open Software License v2.1"
       identifier: biotools:repeatmodeler
 
 input:
@@ -38,13 +37,29 @@ output:
           description: Database files for repeatmodeler
           pattern: "`${prefix}.*`"
           ontologies: []
+  versions_repeatmodeler:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - repeatmodeler:
+          type: string
+          description: The name of the tool
+      - RepeatModeler --version  2>&1 | sed 's/RepeatModeler version //':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - repeatmodeler:
+          type: string
+          description: The name of the tool
+      - RepeatModeler --version  2>&1 | sed 's/RepeatModeler version //':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@GallVp"
 maintainers:

diff --git a/modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test b/modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test
@@ -23,11 +23,12 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out.versions).match("versions") },
-                { assert snapshot(process.out.db[0][1].collect { file(it).name }.sort().toString()).match("db") },
-                { assert snapshot(process.out.db[0][1].findAll { ! ( "$it"[-3..-1] in [ 'nin', 'njs' ] ) }  ).match("stable_md5") }
+                { assert snapshot(
+                    sanitizeOutput(process.out, unstableKeys: ['db']),
+                    process.out.db[0][1].findAll { ! ( "$it"[-3..-1] in [ 'nin', 'njs' ] ) }
+                    ).match() }
             )
         }
 
@@ -49,9 +50,9 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
 

diff --git a/modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test.snap b/modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test.snap
@@ -2,7 +2,7 @@
     "sarscov2-genome_fasta-stub": {
         "content": [
             {
-                "0": [
+                "db": [
                     [
                         {
                             "id": "test"
@@ -19,51 +19,49 @@
                         ]
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,7944637266bc3e2726899eaad5e46c87"
-                ],
+                "versions_repeatmodeler": [
+                    [
+                        "REPEATMODELER_BUILDDATABASE",
+                        "repeatmodeler",
+                        "2.0.5"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-08-03T13:44:38.119214327",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
+    },
+    "sarscov2-genome_fasta": {
+        "content": [
+            {
                 "db": [
                     [
                         {
                             "id": "test"
                         },
                         [
-                            "test.nhr:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "test.nin:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "test.njs:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "test.nnd:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "test.nni:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "test.nog:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "test.nsq:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "test.translation:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            "test.nhr",
+                            "test.nin",
+                            "test.njs",
+                            "test.nnd",
+                            "test.nni",
+                            "test.nog",
+                            "test.nsq",
+                            "test.translation"
                         ]
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,7944637266bc3e2726899eaad5e46c87"
+                "versions_repeatmodeler": [
+                    [
+                        "REPEATMODELER_BUILDDATABASE",
+                        "repeatmodeler",
+                        "2.0.5"
+                    ]
                 ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-04-02T12:06:44.261566"
-    },
-    "versions": {
-        "content": [
-            [
-                "versions.yml:md5,7944637266bc3e2726899eaad5e46c87"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-01-09T15:14:48.807063"
-    },
-    "stable_md5": {
-        "content": [
+            },
             [
                 "test.nhr:md5,1a41cb6d0b00c28f62ad60e75ae2f6fc",
                 "test.nnd:md5,2002e13acf59079a1a5782c918894579",
@@ -73,20 +71,10 @@
                 "test.translation:md5,ccbb119522c09daa976a9015ba999329"
             ]
         ],
+        "timestamp": "2026-08-03T13:44:32.313232604",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-04-23T10:03:41.669433"
-    },
-    "db": {
-        "content": [
-            "[test.nhr, test.nin, test.njs, test.nnd, test.nni, test.nog, test.nsq, test.translation]"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-04-02T12:08:36.94713"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     }
 }
diff --git a/modules/nf-core/repeatmodeler/repeatmodeler/main.nf b/modules/nf-core/repeatmodeler/repeatmodeler/main.nf
@@ -14,7 +14,7 @@ process REPEATMODELER_REPEATMODELER {
     tuple val(meta), path("*.fa") , emit: fasta
     tuple val(meta), path("*.stk"), emit: stk
     tuple val(meta), path("*.log"), emit: log
-    path "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('repeatmodeler'), eval("RepeatModeler --version  2>&1 | sed 's/RepeatModeler version //'") , emit: versions_repeatmodeler, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,18 +25,13 @@ process REPEATMODELER_REPEATMODELER {
     def db_name = file(db[0]).getBaseName()
     """
     RepeatModeler \\
-        -database $db_name \\
-        $args \\
-        -threads $task.cpus
+        -database ${db_name} \\
+        ${args} \\
+        -threads ${task.cpus}
 
     mv ${db_name}-families.fa   ${prefix}.fa
     mv ${db_name}-families.stk  ${prefix}.stk
     mv ${db_name}-rmod.log      ${prefix}.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        repeatmodeler: \$(RepeatModeler --version | sed 's/RepeatModeler version //')
-    END_VERSIONS
     """
 
     stub:
@@ -45,10 +40,5 @@ process REPEATMODELER_REPEATMODELER {
     touch ${prefix}.fa
     touch ${prefix}.stk
     touch ${prefix}.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        repeatmodeler: \$(RepeatModeler --version | sed 's/RepeatModeler version //')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/repeatmodeler/repeatmodeler/meta.yml b/modules/nf-core/repeatmodeler/repeatmodeler/meta.yml
@@ -1,20 +1,18 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "repeatmodeler_repeatmodeler"
-description: Performs de novo transposable element (TE) family identification with
-  RepeatModeler
+description: Performs de novo transposable element (TE) family identification with RepeatModeler
 keywords:
   - genomics
   - fasta
   - repeat
   - transposable element
 tools:
   - "repeatmodeler":
-      description: "RepeatModeler is a de-novo repeat family identification and modeling
-        package."
+      description: "RepeatModeler is a de-novo repeat family identification and modeling package."
       homepage: "https://github.com/Dfam-consortium/RepeatModeler"
       documentation: "https://github.com/Dfam-consortium/RepeatModeler"
       tool_dev_url: "https://github.com/Dfam-consortium/RepeatModeler"
-      licence: ["Open Software License v2.1"]
+      licence:
+        - "Open Software License v2.1"
       identifier: biotools:repeatmodeler
 input:
   - - meta:
@@ -61,13 +59,29 @@ output:
           description: A summarized log of the run
           pattern: "*.log"
           ontologies: []
+  versions_repeatmodeler:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - repeatmodeler:
+          type: string
+          description: The name of the tool
+      - RepeatModeler --version  2>&1 | sed 's/RepeatModeler version //':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - repeatmodeler:
+          type: string
+          description: The name of the tool
+      - RepeatModeler --version  2>&1 | sed 's/RepeatModeler version //':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@GallVp"
 maintainers:

diff --git a/modules/nf-core/repeatmodeler/repeatmodeler/tests/main.nf.test b/modules/nf-core/repeatmodeler/repeatmodeler/tests/main.nf.test
@@ -36,12 +36,10 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out.fasta).match("fasta") },
-                { assert snapshot(process.out.stk).match("stk") },
-                { assert file(process.out.log[0][1]).text.contains('1 families discovered.') },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["log"])).match() },
+                { assert file(process.out.log[0][1]).text.contains('1 families discovered.') }
             )
         }
 
@@ -63,9 +61,9 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }