Adressing Kubras comments for release PR

assets/samplesheet.csv

@@ -1,2 +1,2 @@
 sample,bundle,image
-test_run,https://raw.githubusercontent.com/nf-core/test-datasets/spatialaxe/xenium_bundle.tar.gz
+test_run,https://raw.githubusercontent.com/nf-core/test-datasets/spatialaxe/xenium_bundle.tar.gz,

modules/local/baysor/create_dataset/main.nf

@@ -10,7 +10,7 @@ process BAYSOR_CREATE_DATASET {
 
     output:
     tuple val(meta), path("${prefix}/sampled_transcripts.csv"), emit: sampled_transcripts
-    tuple val("${task.process}"), val('python'), eval("python3 --version | sed 's/Python //'"), topic: versions, emit: versions_python
+    tuple val("${task.process}"), val('baysor'), eval("baysor --version 2>&1 | grep -oP '\\d+\\.\\d+\\.\\d+' || echo unknown"), topic: versions, emit: versions_baysor
 
     when:
     task.ext.when == null || task.ext.when

modules/local/baysor/create_dataset/meta.yml

@@ -53,14 +53,14 @@ output:
           description: Subsampled transcripts CSV used as Baysor input dataset.
           pattern: "*/sampled_transcripts.csv"
           ontologies: []
-  versions_python:
+  versions_baysor:
     - - ${task.process}:
           type: string
           description: The process the versions were collected from
       - python:
           type: string
           description: The tool name
-      - "python3 --version | sed 's/Python //'":
+      - "baysor --version 2>&1 | grep -oP '\\d+\\.\\d+\\.\\d+' || echo unknown":
           type: eval
           description: The expression to obtain the version of the tool
 
@@ -69,10 +69,10 @@ topics:
     - - ${task.process}:
           type: string
           description: The process the versions were collected from
-      - python:
+      - baysor:
           type: string
           description: The tool name
-      - "python3 --version | sed 's/Python //'":
+      - "baysor --version 2>&1 | grep -oP '\\d+\\.\\d+\\.\\d+' || echo unknown":
           type: eval
           description: The expression to obtain the version of the tool
 

modules/local/baysor/create_dataset/tests/main.nf.test

@@ -29,7 +29,7 @@ nextflow_process {
                 { assert process.success },
                 { assert file(process.out.sampled_transcripts[0][1]).exists() },
                 { assert file(process.out.sampled_transcripts[0][1]).name == "sampled_transcripts.csv" },
-                { assert snapshot(process.out.versions_python).match("versions") }
+                { assert snapshot(process.out.versions_baysor).match("versions") }
             )
         }
     }
@@ -53,7 +53,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions_python).match("versions_stub") }
+                { assert snapshot(process.out.versions_baysor).match("versions_stub") }
             )
         }
     }

modules/local/baysor/create_dataset/tests/main.nf.test.snap

@@ -4,31 +4,31 @@
             [
                 [
                     "BAYSOR_CREATE_DATASET",
-                    "python",
-                    "3.11.2"
+                    "baysor",
+                    "0.7.1"
                 ]
             ]
         ],
+        "timestamp": "2026-06-17T13:16:19.929465332",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-03-21T03:57:19.078934192"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.2"
+        }
     },
     "versions": {
         "content": [
             [
                 [
                     "BAYSOR_CREATE_DATASET",
-                    "python",
-                    "3.11.2"
+                    "baysor",
+                    "0.7.1"
                 ]
             ]
         ],
+        "timestamp": "2026-06-17T13:16:11.036406226",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-03-21T05:05:40.700569871"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.2"
+        }
     }
 }

modules/local/baysor/preprocess/meta.yml

@@ -48,21 +48,39 @@ input:
         if no limit is specified, the default minimum value will be 0.0
 
 output:
-  - - transcripts_parquet:
-        - meta:
+  transcripts_file:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test' ]
-        - "*.csv":
+      - "*.csv":
           type: file
           description: filtered transcripts CSV (for Baysor 0.7.1 Parquet.jl compatibility)
           pattern: "filtered_transcripts.csv"
 
-  - - versions_python:
-      type: tuple
-      description: Python version emitted via topic channel
-      pattern: "topic: versions"
+  versions_python:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - python:
+          type: string
+          description: The tool name
+      - "python3 --version | sed 's/Python //'":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - python:
+          type: string
+          description: The tool name
+      - "python3 --version | sed 's/Python //'":
+          type: eval
+          description: The expression to obtain the version of the tool
 
 authors:
   - "@khersameesh24"

modules/local/baysor/preview/meta.yml

@@ -31,22 +31,38 @@ input:
 
 ## segmentation results
 output:
-  - preview_html:
-      - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test' ]
-      - "preview.html":
+  preview_html:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+    - "preview.html":
         type: file
         description: segmentation preview
         pattern: "preview.html"
+  versions_baysor:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - python:
+          type: string
+          description: The tool name
+      - "baysor --version 2>&1 | grep -oP '\\d+\\.\\d+\\.\\d+' || echo unknown":
+          type: eval
+          description: The expression to obtain the version of the tool
 
-  - preview_log:
-    type: file
-    description: |
-      Log file with summary statistics of preview
-    pattern: "preview_preview_log.log"
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - baysor:
+          type: string
+          description: The tool name
+      - "baysor --version 2>&1 | grep -oP '\\d+\\.\\d+\\.\\d+' || echo unknown":
+          type: eval
+          description: The expression to obtain the version of the tool
 
 authors:
   - "@sebgoti8"

modules/local/baysor/run/meta.yml

@@ -75,10 +75,28 @@ output:
       Statistics of segmented cells
     pattern: "segmentation_cell_stats.csv"
 
-  - versions:
-    type: file
-    description: File containing software versions
-    pattern: "versions.yml"
+  - versions_baysor:
+      - - ${task.process}:
+            type: string
+            description: The process the versions were collected from
+        - python:
+            type: string
+            description: The tool name
+        - "baysor --version 2>&1 | grep -oP '\\d+\\.\\d+\\.\\d+' || echo unknown":
+            type: eval
+            description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - python:
+          type: string
+          description: The tool name
+      - "baysor --version 2>&1 | grep -oP '\\d+\\.\\d+\\.\\d+' || echo unknown":
+          type: eval
+          description: The expression to obtain the version of the tool
 
 authors:
   - "@sebgoti8"

modules/local/baysor/segfree/meta.yml

@@ -2,6 +2,8 @@ name: "baysor_segfree"
 description: Extract neighborhood composition vectors (NVCs) from a dataset.
 keywords:
   - neighborhood
+  - baysor
+  - segmentation_free
 tools:
   - "baysor":
     description: "Baysor is a tool that segments cells using spatial gene expression maps. Optionally, segmentation masks can be given as additional input."
@@ -30,22 +32,40 @@ input:
 
 ## neighborhood composition vectors
 output:
-  - preview_html:
-      - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test' ]
-      - "ncvs.loom":
+  ncvs:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+    - "${prefix}/ncvs.loom":
         type: file
-        description: loom file with neighborhood results
-        pattern: "ncvs.loom"
+        description: |
+          Segmenation file in loom format
+        pattern: "${prefix}/ncvs.loom"
+
+  versions_baysor:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - python:
+          type: string
+          description: The tool name
+      - "baysor --version 2>&1 | grep -oP '\\d+\\.\\d+\\.\\d+' || echo unknown":
+          type: eval
+          description: The expression to obtain the version of the tool
 
-  - ncvs_log:
-    type: file
-    description: |
-      Log file with summary statistics
-    pattern: "ncvs_segfree_log.log"
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - python:
+          type: string
+          description: The tool name
+      - "baysor --version 2>&1 | grep -oP '\\d+\\.\\d+\\.\\d+' || echo unknown":
+          type: eval
+          description: The expression to obtain the version of the tool
 
 authors:
   - "@sebgoti8"

modules/local/ficture/model/meta.yml

@@ -2,8 +2,9 @@ name: ficture
 description: FICTURE is a software tool that performs segmentation-free analysis of submicron-resolution analysis of spatial transcriptomics data.
 keywords:
   - spatial
-  - segmentation free
+  - segmentation_free
   - imaging
+  - ficture
 tools:
   - ficture:
       description: |
@@ -31,14 +32,38 @@ input:
         type: file
         description: Another file contains the (unique) names of genes that should be used in analysis. The required columns is just gene (including the header), the naming of genes should match the gene column in the transcript file. If your data contain negative control probes or if you would like to remove certain genes this is where you can specify.
 output:
-  - results:
-      type: file
-      description: Files containing the results of FICTURE
-      pattern: "${meta.id}/results/*"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+  results:
+    - - meta:
+        type: map
+        description: |
+          Groovy Map containing run information
+          e.g. [id:'sample']
+    - results:
+        type: file
+        description: Files containing the results of FICTURE
+        pattern: "${meta.id}/results/*"
+  versions_ficture:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - python:
+          type: string
+          description: The tool name
+      - "pip show ficture | sed -n 's/^Version: //p'":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - python:
+          type: string
+          description: The tool name
+      - "pip show ficture | sed -n 's/^Version: //p'":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@khersameesh24"
   - "@heylf"