nf-core · LouisLeNezet · Jul 6, 2026 · Jul 6, 2026 · Jul 6, 2026 · Jul 6, 2026
diff --git a/modules/nf-core/metaspace/converter/main.nf b/modules/nf-core/metaspace/converter/main.nf
@@ -17,7 +17,7 @@ process METASPACE_CONVERTER {
     output:
     path("AnnData_${ds_id}.h5ad")    , emit: adata_object
     path("SpatialData_${ds_id}.zarr"), emit: sdata_object
-    path("versions.yml")             , emit: versions
+    path("versions.yml")             , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/nf-core/metaspace/converter/meta.yml b/modules/nf-core/metaspace/converter/meta.yml
@@ -19,7 +19,8 @@ tools:
 input:
   - ds_id:
       type: string
-      description: METASPACE dataset identifier to retrieve and convert to AnnData and SpatialData formats.
+      description: METASPACE dataset identifier to retrieve and convert to AnnData
+        and SpatialData formats.
   - database_name_:
       type: string
       description: Name of the metabolite annotation database to use (e.g., HMDB)
@@ -28,7 +29,8 @@ input:
       description: Version of the annotation database to use (e.g., v4)
   - fdr_:
       type: string
-      description: False Discovery Rate threshold for filtering metabolite annotations.
+      description: False Discovery Rate threshold for filtering metabolite
+        annotations.
       pattern: "^(0(\\.[0-9]+)?|1(\\.0+)?)$"
   - use_tic_:
       type: string
@@ -57,7 +59,15 @@ output:
         description: File containing software versions
         pattern: "versions.yml"
         ontologies:
-          - edam: http://edamontology.org/format_3750
+          - edam: http://edamontology.org/format_3750 # YAML
+topics:
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@bisho2122"
 maintainers:

diff --git a/modules/nf-core/metaspace/converter/tests/main.nf.test b/modules/nf-core/metaspace/converter/tests/main.nf.test
@@ -55,7 +55,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }

diff --git a/modules/nf-core/metaspace/converter/tests/main.nf.test.snap b/modules/nf-core/metaspace/converter/tests/main.nf.test.snap
@@ -2,15 +2,6 @@
     "metaspace_converter - stub": {
         "content": [
             {
-                "0": [
-                    "AnnData_2022-08-05_17h28m56s.h5ad:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ],
-                "1": [
-                    "SpatialData_2022-08-05_17h28m56s.zarr:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ],
-                "2": [
-                    "versions.yml:md5,4451269b2937114efdd8f7e221598701"
-                ],
                 "adata_object": [
                     "AnnData_2022-08-05_17h28m56s.h5ad:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
@@ -22,26 +13,26 @@
                 ]
             }
         ],
-        "timestamp": "2025-03-27T16:29:42.150424618",
+        "timestamp": "2026-07-06T14:13:29.191028124",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     },
     "metaspace_converter_test": {
         "content": [
             [
-                "AnnData_2022-08-05_17h28m56s.h5ad:md5,a6036323aa5451f55a6c3bca4eb65853"
+                "AnnData_2022-08-05_17h28m56s.h5ad:md5,68da810daf425d58d0ca32d53c01fbd1"
             ],
-            "zmetadata:md5,42c7001eb2356c9d643527d141a25b3f",
+            "zmetadata:md5,838a1c70924eed6b0286e15baee95337",
             [
                 "versions.yml:md5,4451269b2937114efdd8f7e221598701"
             ]
         ],
-        "timestamp": "2026-02-23T11:11:31.706371897",
+        "timestamp": "2026-07-06T14:16:07.135232143",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     }
 }
diff --git a/modules/nf-core/metaspace/download/main.nf b/modules/nf-core/metaspace/download/main.nf
@@ -10,9 +10,9 @@ process METASPACE_DOWNLOAD {
     tuple val(dataset_id), val(database), val(version)
 
     output:
-    path "${dataset_id}_*.csv", optional: true, emit: results
-    stdout                                      emit: log  // check meta.yml for see how to use!
-    path 'versions.yml'                       , emit: versions
+    path "${dataset_id}_*.csv", emit: results, optional: true
+    stdout                      emit: log
+    path "versions.yml"       , emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/nf-core/metaspace/download/meta.yml b/modules/nf-core/metaspace/download/meta.yml
@@ -1,20 +1,22 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "metaspace_download"
-description: A module to download dataset results from the METASPACE platform and
-  save them as CSV files, using a containerized Python script. Inputs are provided
-  via a CSV file or a list of datasets, with results saved to a specified output directory.
+description: A module to download dataset results from the METASPACE platform
+  and save them as CSV files, using a containerized Python script. Inputs are
+  provided via a CSV file or a list of datasets, with results saved to a
+  specified output directory.
 keywords:
   - metaspace
   - metabolite annotation
   - data-download
   - csv
 tools:
   - metaspace2020:
-      description: Python package providing programmatic access to the METASPACE platform
+      description: Python package providing programmatic access to the METASPACE
+        platform
       homepage: https://metaspace2020.readthedocs.io
       documentation: https://metaspace2020.readthedocs.io
       tool_dev_url: https://github.com/metaspace2020/metaspace/tree/master/metaspace/python-client
-      licence: ["Apache-2.0 license"]
+      licence:
+        - "Apache-2.0 license"
       identifier: ""
 input:
   - - dataset_id:
@@ -47,10 +49,9 @@ output:
           Filename format is '{dataset_id}_*.csv'.
         pattern: "*.csv"
         ontologies:
-          - edam: "http://edamontology.org/format_3752:latest" # CSV format
           - edam: http://edamontology.org/format_3752 # CSV
   log:
-    - "emit:":
+    - "emit: log":
         type: string
         description: |
           The standard output (stdout) of the script, containing log messages.
@@ -68,12 +69,17 @@ output:
   versions:
     - versions.yml:
         type: file
-        description: |
-          YAML file containing the versions of the tools used in the pipeline.
-          This file is automatically generated by the pipeline and should not be modified.
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+topics:
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
         pattern: "versions.yml"
         ontologies:
-          - edam: "http://edamontology.org/format_3475" # YAML format
           - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@Dewey-Wang"

diff --git a/modules/nf-core/metaspace/download/tests/main.nf.test b/modules/nf-core/metaspace/download/tests/main.nf.test
@@ -14,7 +14,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.from([
+                input[0] = channel.from([
                     ['2022-08-05_17h28m56s', 'KEGG', null],
                     ['2022-08-05_17h28m56s', null, null]
                 ])
@@ -25,7 +25,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
@@ -34,7 +34,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.from([
+                input[0] = channel.from([
                     ['2022-08-05_17h28m56s', 'KEGG', null],
                     ['2022-08-05_17h28m56s', null, null],
                     [null, 'KEGG', null] // Missing dataset_id
@@ -65,7 +65,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.from([
+                input[0] = channel.from([
                     ['2022-08-05_17h28m56s', 'KEGG', null],
                     ['2022-08-05_17h28m56s', null, null]
                 ])
@@ -75,7 +75,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }

diff --git a/modules/nf-core/metaspace/download/tests/main.nf.test.snap b/modules/nf-core/metaspace/download/tests/main.nf.test.snap
@@ -3,62 +3,38 @@
         "content": [
             "      raise ValueError(\"Error: input csv or datasets contains an entry with missing dataset_id.\")"
         ],
+        "timestamp": "2025-03-27T23:59:56.527423",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-27T23:59:56.527423"
+        }
     },
     "metaspace/download - datasets": {
         "content": [
             {
-                "0": [
-                    "2022-08-05_17h28m56s_KEGG_v1.csv:md5,44a3760625f0e2f9aeee5639bd973d9b",
-                    "2022-08-05_17h28m56s_all_databases.csv:md5,93496262735b9f316f82c843c773a944"
-                ],
-                "1": [
-                    "Processing dataset_id: 2022-08-05_17h28m56s, database: KEGG, version: None\nFetching dataset: 2022-08-05_17h28m56s\nAvailable databases and versions:\n  - HMDB-cotton v4\n  - LipidMaps 2017-12-12\n  - KEGG v1\n  - BraChemDB 2018-01\nProcessing database: KEGG, version: v1\n\u2705 2022-08-05_17h28m56s with KEGG database are saved to 2022-08-05_17h28m56s_KEGG_v1.csv\nversions.yml file has been generated.\n",
-                    "Processing dataset_id: 2022-08-05_17h28m56s, database: None, version: None\nFetching dataset: 2022-08-05_17h28m56s\nAvailable databases and versions:\n  - HMDB-cotton v4\n  - LipidMaps 2017-12-12\n  - KEGG v1\n  - BraChemDB 2018-01\nProcessing database: HMDB-cotton, version: v4\nProcessing database: LipidMaps, version: 2017-12-12\nProcessing database: KEGG, version: v1\nProcessing database: BraChemDB, version: 2018-01\n\u2705 2022-08-05_17h28m56s with all database are saved to 2022-08-05_17h28m56s_all_databases.csv\nversions.yml file has been generated.\n"
-                ],
-                "2": [
-                    "versions.yml:md5,194f18da1ce360bf7f6ba4afe4964a89",
-                    "versions.yml:md5,194f18da1ce360bf7f6ba4afe4964a89"
-                ],
                 "log": [
                     "Processing dataset_id: 2022-08-05_17h28m56s, database: KEGG, version: None\nFetching dataset: 2022-08-05_17h28m56s\nAvailable databases and versions:\n  - HMDB-cotton v4\n  - LipidMaps 2017-12-12\n  - KEGG v1\n  - BraChemDB 2018-01\nProcessing database: KEGG, version: v1\n\u2705 2022-08-05_17h28m56s with KEGG database are saved to 2022-08-05_17h28m56s_KEGG_v1.csv\nversions.yml file has been generated.\n",
                     "Processing dataset_id: 2022-08-05_17h28m56s, database: None, version: None\nFetching dataset: 2022-08-05_17h28m56s\nAvailable databases and versions:\n  - HMDB-cotton v4\n  - LipidMaps 2017-12-12\n  - KEGG v1\n  - BraChemDB 2018-01\nProcessing database: HMDB-cotton, version: v4\nProcessing database: LipidMaps, version: 2017-12-12\nProcessing database: KEGG, version: v1\nProcessing database: BraChemDB, version: 2018-01\n\u2705 2022-08-05_17h28m56s with all database are saved to 2022-08-05_17h28m56s_all_databases.csv\nversions.yml file has been generated.\n"
                 ],
                 "results": [
-                    "2022-08-05_17h28m56s_KEGG_v1.csv:md5,44a3760625f0e2f9aeee5639bd973d9b",
-                    "2022-08-05_17h28m56s_all_databases.csv:md5,93496262735b9f316f82c843c773a944"
+                    "2022-08-05_17h28m56s_KEGG_v1.csv:md5,fa5b95e299a02e79cc16bf3d1c9564bf",
+                    "2022-08-05_17h28m56s_all_databases.csv:md5,4ccd94e8285efaf286ca0b2a8e9f261e"
                 ],
                 "versions": [
                     "versions.yml:md5,194f18da1ce360bf7f6ba4afe4964a89",
                     "versions.yml:md5,194f18da1ce360bf7f6ba4afe4964a89"
                 ]
             }
         ],
+        "timestamp": "2026-07-06T14:13:41.36299967",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-04-05T14:05:56.321679"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
+        }
     },
     "metaspace/download - stub": {
         "content": [
             {
-                "0": [
-                    "2022-08-05_17h28m56s_KEGG_all_versions.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
-                    "2022-08-05_17h28m56s_all_databases.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ],
-                "1": [
-                    "",
-                    ""
-                ],
-                "2": [
-                    "versions.yml:md5,83b3435f6de10ae175f191530d4389dd",
-                    "versions.yml:md5,83b3435f6de10ae175f191530d4389dd"
-                ],
                 "log": [
                     "",
                     ""
@@ -73,10 +49,10 @@
                 ]
             }
         ],
+        "timestamp": "2026-07-06T14:14:02.823842826",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-04-05T14:15:24.315874"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
+        }
     }
 }