fastavalidator topics migration

modules/nf-core/fastavalidator/main.nf

@@ -13,12 +13,18 @@ process FASTAVALIDATOR {
     output:
     tuple val(meta), path('*.success.log')  , emit: success_log , optional: true
     tuple val(meta), path('*.error.log')    , emit: error_log   , optional: true
-    path "versions.yml"                     , emit: versions
+    tuple val("${task.process}"), val('py_fasta_validator'), eval('py_fasta_validator --version | cut -d" " -f3'), emit: versions_py_fasta_validator, topic: versions
+
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "Fastavalidator module does not support Conda. Please use Docker / Singularity instead."
+    }
+
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     py_fasta_validator \\
@@ -41,22 +47,17 @@ process FASTAVALIDATOR {
         echo "Validation successful..." \\
             > "${prefix}.success.log"
     fi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        py_fasta_validator: \$(py_fasta_validator -v | sed 's/.* version //')
-    END_VERSIONS
     """
 
     stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "Fastavalidator module does not support Conda. Please use Docker / Singularity instead."
+    }
+
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     echo "Validation successful..." \\
         > "${prefix}.success.log"
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        py_fasta_validator: \$(py_fasta_validator -v | sed 's/.* version //')
-    END_VERSIONS
     """
 }

modules/nf-core/fastavalidator/meta.yml

@@ -17,7 +17,8 @@ tools:
       documentation: "https://github.com/linsalrob/py_fasta_validator"
       tool_dev_url: "https://github.com/linsalrob/py_fasta_validator"
       doi: "10.5281/zenodo.5002710"
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - - meta:
@@ -53,13 +54,27 @@ output:
           description: Log file for failed validation
           pattern: "*.error.log"
           ontologies: []
+  versions_py_fasta_validator:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - py_fasta_validator:
+          type: string
+          description: The name of the tool
+      - py_fasta_validator --version | cut -d" " -f3:
+          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
+      - py_fasta_validator:
+          type: string
+          description: The name of the tool
+      - py_fasta_validator --version | cut -d" " -f3:
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@gallvp"
 maintainers:

modules/nf-core/fastavalidator/tests/main.nf.test.snap

@@ -15,7 +15,11 @@
 
                 ],
                 "2": [
-                    "versions.yml:md5,05aa059840b3b4dd6d88bc1e4bf976d7"
+                    [
+                        "FASTAVALIDATOR",
+                        "py_fasta_validator",
+                        "0.6"
+                    ]
                 ],
                 "error_log": [
 
@@ -29,12 +33,20 @@
                         "test.success.log:md5,b0b859eda1db5cd43915846e00ebc22c"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,05aa059840b3b4dd6d88bc1e4bf976d7"
+                "versions_py_fasta_validator": [
+                    [
+                        "FASTAVALIDATOR",
+                        "py_fasta_validator",
+                        "0.6"
+                    ]
                 ]
             }
         ],
-        "timestamp": "2023-11-28T11:23:25.106872"
+        "timestamp": "2026-03-15T21:53:50.62913298",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "sarscov2-gff3-invalid": {
         "content": [
@@ -52,7 +64,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,05aa059840b3b4dd6d88bc1e4bf976d7"
+                    [
+                        "FASTAVALIDATOR",
+                        "py_fasta_validator",
+                        "0.6"
+                    ]
                 ],
                 "error_log": [
                     [
@@ -66,11 +82,19 @@
                 "success_log": [
 
                 ],
-                "versions": [
-                    "versions.yml:md5,05aa059840b3b4dd6d88bc1e4bf976d7"
+                "versions_py_fasta_validator": [
+                    [
+                        "FASTAVALIDATOR",
+                        "py_fasta_validator",
+                        "0.6"
+                    ]
                 ]
             }
         ],
-        "timestamp": "2023-11-28T11:23:29.40324"
+        "timestamp": "2026-03-15T21:53:59.053193204",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }