From d7532d8066c81676ca70fea1aa30681dada9d219 Mon Sep 17 00:00:00 2001
From: f641l <florian.heyl@dkfz-heidelberg.de>
Date: Tue, 16 Jun 2026 18:38:23 +0200
Subject: [PATCH 1/8] addressing kubras comments

---
 assets/samplesheet.csv                        |  2 +-
 modules/local/baysor/create_dataset/main.nf   |  2 +-
 modules/local/baysor/create_dataset/meta.yml  | 14 ++------------
 modules/local/baysor/run/meta.yml             | 15 +++++++++++----
 modules/local/baysor/segfree/meta.yml         | 14 ++++++++++++++
 modules/local/ficture/model/meta.yml          | 19 ++++++++++++++-----
 modules/local/ficture/preprocess/meta.yml     | 19 ++++++++++++++-----
 modules/local/parquet_to_csv/main.nf          | 11 -----------
 modules/local/proseg/proseg2baysor/meta.yml   | 15 +++++++++++----
 modules/local/resolift/meta.yml               | 15 +++++++++++----
 modules/local/segger/create_dataset/meta.yml  | 15 +++++++++++----
 modules/local/segger/predict/meta.yml         | 15 +++++++++++----
 modules/local/segger/train/meta.yml           | 18 +++++++++++++-----
 .../meta.yml                                  |  4 ----
 14 files changed, 114 insertions(+), 64 deletions(-)

diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
index d30b6fdd..72ad34f0 100644
--- a/assets/samplesheet.csv
+++ b/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,
diff --git a/modules/local/baysor/create_dataset/main.nf b/modules/local/baysor/create_dataset/main.nf
index 98046161..7e15ce8b 100644
--- a/modules/local/baysor/create_dataset/main.nf
+++ b/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
diff --git a/modules/local/baysor/create_dataset/meta.yml b/modules/local/baysor/create_dataset/meta.yml
index 2b40e712..c5091da2 100644
--- a/modules/local/baysor/create_dataset/meta.yml
+++ b/modules/local/baysor/create_dataset/meta.yml
@@ -53,26 +53,16 @@ output:
           description: Subsampled transcripts CSV used as Baysor input dataset.
           pattern: "*/sampled_transcripts.csv"
           ontologies: []
-  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:
+  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
 
diff --git a/modules/local/baysor/run/meta.yml b/modules/local/baysor/run/meta.yml
index 455bade3..584c40d9 100644
--- a/modules/local/baysor/run/meta.yml
+++ b/modules/local/baysor/run/meta.yml
@@ -75,10 +75,17 @@ output:
       Statistics of segmented cells
     pattern: "segmentation_cell_stats.csv"
 
-  - versions:
-    type: file
-    description: File containing software versions
-    pattern: "versions.yml"
+topics:
+  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
 
 authors:
   - "@sebgoti8"
diff --git a/modules/local/baysor/segfree/meta.yml b/modules/local/baysor/segfree/meta.yml
index 9161c1ce..8d4e93f9 100644
--- a/modules/local/baysor/segfree/meta.yml
+++ b/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."
@@ -47,6 +49,18 @@ output:
       Log file with summary statistics
     pattern: "ncvs_segfree_log.log"
 
+topics:
+  versions_baysor:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - python:
+          type: string
+          description: The tool name
+      - "baysor --version 2>&1 | grep -oP '\\d+\\.\\d+\\.\\d+' || echo unknown":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@sebgoti8"
   - "@khersameesh24"
diff --git a/modules/local/ficture/model/meta.yml b/modules/local/ficture/model/meta.yml
index 5b2abcc1..edde1c11 100644
--- a/modules/local/ficture/model/meta.yml
+++ b/modules/local/ficture/model/meta.yml
@@ -2,8 +2,9 @@ name: ficture
 description: FICTURE is a software tool that performs segmentation-free analysis of submicron-resolution analysis of spatial transcriptomics data.
 keywords:
   - spatial
-  - segmentation free
+  - segmentation_free
   - imaging
+  - ficture
 tools:
   - ficture:
       description: |
@@ -35,10 +36,18 @@ output:
       type: file
       description: Files containing the results of FICTURE
       pattern: "${meta.id}/results/*"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+topics:
+  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
+
 authors:
   - "@khersameesh24"
   - "@heylf"
diff --git a/modules/local/ficture/preprocess/meta.yml b/modules/local/ficture/preprocess/meta.yml
index 89366c32..c8eefcba 100644
--- a/modules/local/ficture/preprocess/meta.yml
+++ b/modules/local/ficture/preprocess/meta.yml
@@ -2,9 +2,10 @@ name: ficture_preprocessing
 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
   - preprocessing
+  - ficture
 tools:
   - ficture:
       description: |
@@ -41,10 +42,18 @@ output:
       type: file
       description: Another file contains the (unique) names of genes that should be used for FICUTRE
       pattern: "feature.clean.tsv.gz"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+topics:
+  versions_ficture:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - python:
+          type: string
+          description: The tool name
+      - "pip show ficture | sed -n 's/^Version: //p'":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@khersameesh24"
   - "@heylf"
diff --git a/modules/local/parquet_to_csv/main.nf b/modules/local/parquet_to_csv/main.nf
index abfb246e..26c613e3 100644
--- a/modules/local/parquet_to_csv/main.nf
+++ b/modules/local/parquet_to_csv/main.nf
@@ -1,14 +1,3 @@
-/*
- * PARQUET_TO_CSV: Convert parquet file to CSV for tools with old Parquet readers.
- *
- * Input:
- *   - meta: Sample metadata map
- *   - parquet: Parquet file to convert
- *
- * Output:
- *   - csv: Converted CSV file
- *   - versions: Software versions
- */
 process PARQUET_TO_CSV {
     tag "$meta.id"
     label 'process_low'
diff --git a/modules/local/proseg/proseg2baysor/meta.yml b/modules/local/proseg/proseg2baysor/meta.yml
index e423e97b..8659b399 100644
--- a/modules/local/proseg/proseg2baysor/meta.yml
+++ b/modules/local/proseg/proseg2baysor/meta.yml
@@ -45,10 +45,17 @@ output:
         type: file
         description: Transcript ids, genes, revised positions, assignment probability
         pattern: "xr-transcript-metadata.csv"
-  - - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+topics:
+  versions_proseg:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - python:
+          type: string
+          description: The tool name
+      - "proseg --version | sed 's/proseg //'":
+          type: eval
+          description: The expression to obtain the version of the tool
 
 authors:
   - "@khersameesh24"
diff --git a/modules/local/resolift/meta.yml b/modules/local/resolift/meta.yml
index 673e23fc..2488c24c 100644
--- a/modules/local/resolift/meta.yml
+++ b/modules/local/resolift/meta.yml
@@ -35,10 +35,17 @@ output:
         type: file
         description: Path to save the upscaled TIFF file.
         pattern: ".tiff"
-  - - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+topics:
+  versions_resolift:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - python:
+          type: string
+          description: The tool name
+      - "pip show resolift | sed -n 's/^Version: //p'":
+          type: eval
+          description: The expression to obtain the version of the tool
 
 authors:
   - "@kubranarci"
diff --git a/modules/local/segger/create_dataset/meta.yml b/modules/local/segger/create_dataset/meta.yml
index f1573869..16f1651c 100644
--- a/modules/local/segger/create_dataset/meta.yml
+++ b/modules/local/segger/create_dataset/meta.yml
@@ -32,10 +32,17 @@ output:
     - datasetdir:
         description: |
           Directory to save the processed Segger dataset (in PyTorch Geometric format).
-  - - versions:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
+topics:
+  versions_segger:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - python:
+          type: string
+          description: The tool name
+      - "pip show segger | sed -n 's/^Version: //p'":
+          type: eval
+          description: The expression to obtain the version of the tool
 
 authors:
   - "@tobiaspk"
diff --git a/modules/local/segger/predict/meta.yml b/modules/local/segger/predict/meta.yml
index fab577b2..085b0a2b 100644
--- a/modules/local/segger/predict/meta.yml
+++ b/modules/local/segger/predict/meta.yml
@@ -45,10 +45,17 @@ output:
     - benchmarks_dir:
         description: |
           Directory to save the segmentation results, including cell boundaries and associations.
-  - - versions:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
+topics:
+  versions_segger:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - python:
+          type: string
+          description: The tool name
+      - "pip show segger | sed -n 's/^Version: //p'":
+          type: eval
+          description: The expression to obtain the version of the tool
 
 authors:
   - "@tobiaspk"
diff --git a/modules/local/segger/train/meta.yml b/modules/local/segger/train/meta.yml
index 40b838b8..c1a79d80 100644
--- a/modules/local/segger/train/meta.yml
+++ b/modules/local/segger/train/meta.yml
@@ -4,7 +4,7 @@ keywords:
   - segmentation
   - xenium
   - imaging
-  - model-training
+  - model_training
 tools:
   - "segger":
       description: "Segger uses graph neural networks and heterogeneous graphs to offer efficient cell segmentation at unmatched precision and accuracy."
@@ -34,10 +34,18 @@ output:
         type: directory
         description: |
           Directory to save the trained model and checkpoints.
-  - - versions:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
+topics:
+  versions_segger:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - python:
+          type: string
+          description: The tool name
+      - "pip show segger | sed -n 's/^Version: //p'":
+          type: eval
+          description: The expression to obtain the version of the tool
+
 
 authors:
   - "@tobiaspk"
diff --git a/subworkflows/local/xeniumranger_resegment_morphology_ome_tif/meta.yml b/subworkflows/local/xeniumranger_resegment_morphology_ome_tif/meta.yml
index db6a07a8..3af4f3aa 100644
--- a/subworkflows/local/xeniumranger_resegment_morphology_ome_tif/meta.yml
+++ b/subworkflows/local/xeniumranger_resegment_morphology_ome_tif/meta.yml
@@ -27,10 +27,6 @@ output:
       description: |
         the coordinate space in which xeniumranger import-segmentation was run
         Structure: [ val("pixels") ]
-  - versions:
-      description: |
-        Files containing software versions
-        Structure: [ path(versions.yml) ]
 authors:
   - "@khersameesh24"
 maintainers:

From 614c504340cca10f484eedc559f60f0e88daaaf3 Mon Sep 17 00:00:00 2001
From: f641l <florian.heyl@dkfz-heidelberg.de>
Date: Wed, 17 Jun 2026 10:47:53 +0200
Subject: [PATCH 2/8] prettier

---
 modules/local/segger/train/meta.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/local/segger/train/meta.yml b/modules/local/segger/train/meta.yml
index c1a79d80..d73e9ba2 100644
--- a/modules/local/segger/train/meta.yml
+++ b/modules/local/segger/train/meta.yml
@@ -46,7 +46,6 @@ topics:
           type: eval
           description: The expression to obtain the version of the tool
 
-
 authors:
   - "@tobiaspk"
   - "@khersameesh24"

From 75bf41f3f3d2d0b53df45ca42d2e0d27a775a9dc Mon Sep 17 00:00:00 2001
From: f641l <florian.heyl@dkfz-heidelberg.de>
Date: Wed, 17 Jun 2026 11:03:17 +0200
Subject: [PATCH 3/8] update snapshot

---
 .../create_dataset/tests/main.nf.test.snap    | 36 ++++++-------------
 1 file changed, 10 insertions(+), 26 deletions(-)

diff --git a/modules/local/baysor/create_dataset/tests/main.nf.test.snap b/modules/local/baysor/create_dataset/tests/main.nf.test.snap
index 6a0b446e..2a585c4d 100644
--- a/modules/local/baysor/create_dataset/tests/main.nf.test.snap
+++ b/modules/local/baysor/create_dataset/tests/main.nf.test.snap
@@ -1,34 +1,18 @@
 {
     "versions_stub": {
-        "content": [
-            [
-                [
-                    "BAYSOR_CREATE_DATASET",
-                    "python",
-                    "3.11.2"
-                ]
-            ]
-        ],
+        "content": null,
+        "timestamp": "2026-06-17T10:57:59.488545662",
         "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"
-                ]
-            ]
-        ],
+        "content": null,
+        "timestamp": "2026-06-17T10:57:49.73564258",
         "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"
+        }
     }
 }
\ No newline at end of file

From 17132163c7ca78a92807b1a075457ab652dde542 Mon Sep 17 00:00:00 2001
From: f641l <florian.heyl@dkfz-heidelberg.de>
Date: Wed, 17 Jun 2026 11:15:42 +0200
Subject: [PATCH 4/8] update snapshot

---
 tests/preview_mode.nf.test.snap | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/preview_mode.nf.test.snap b/tests/preview_mode.nf.test.snap
index 03a826e2..e44ff636 100644
--- a/tests/preview_mode.nf.test.snap
+++ b/tests/preview_mode.nf.test.snap
@@ -3,7 +3,7 @@
         "content": [
             {
                 "BAYSOR_CREATE_DATASET": {
-                    "python": "3.11.2"
+                    "baysor": "0.7.1"
                 },
                 "BAYSOR_PREVIEW": {
                     "baysor": "0.7.1"
@@ -111,10 +111,10 @@
                 "umap_mqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
-        "timestamp": "2026-05-18T22:01:44.940462508",
+        "timestamp": "2026-06-17T11:15:30.764424637",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
+            "nextflow": "26.04.2"
         }
     }
 }
\ No newline at end of file

From 717d5421b30c8ed422156e42f2da2a75a3f5c08e Mon Sep 17 00:00:00 2001
From: f641l <florian.heyl@dkfz-heidelberg.de>
Date: Wed, 17 Jun 2026 11:56:09 +0200
Subject: [PATCH 5/8] sorry forgot some file sto push

---
 subworkflows/local/baysor_generate_preview/meta.yml         | 4 ----
 subworkflows/local/baysor_generate_segfree/meta.yml         | 4 ----
 .../local/baysor_run_prior_segmentation_mask/meta.yml       | 4 ----
 subworkflows/local/baysor_run_transcripts_parquet/meta.yml  | 4 ----
 .../local/cellpose_baysor_import_segmentation/meta.yml      | 4 ----
 .../local/cellpose_resolift_morphology_ome_tif/meta.yml     | 4 ----
 subworkflows/local/ficture_preprocess_model/meta.yml        | 4 ----
 subworkflows/local/opt_flip_track_stat/meta.yml             | 6 ------
 subworkflows/local/proseg_preset_proseg2baysor/meta.yml     | 4 ----
 subworkflows/local/segger_create_train_predict/meta.yml     | 4 ----
 subworkflows/local/spatialdata_write_meta_merge/meta.yml    | 4 ----
 .../meta.yml                                                | 4 ----
 subworkflows/local/xeniumranger_relabel_resegment/meta.yml  | 4 ----
 13 files changed, 54 deletions(-)

diff --git a/subworkflows/local/baysor_generate_preview/meta.yml b/subworkflows/local/baysor_generate_preview/meta.yml
index 3ca9fa8e..5807c233 100644
--- a/subworkflows/local/baysor_generate_preview/meta.yml
+++ b/subworkflows/local/baysor_generate_preview/meta.yml
@@ -28,10 +28,6 @@ output:
       description: |
         Preview html file generated with the baysor preview command
         Structure: [ val(meta), path("path-to-preview.html") ]
-  - versions:
-      description: |
-        Files containing software versions
-        Structure: [ path(versions.yml) ]
 authors:
   - "@khersameesh24"
 maintainers:
diff --git a/subworkflows/local/baysor_generate_segfree/meta.yml b/subworkflows/local/baysor_generate_segfree/meta.yml
index f8c951c9..b312ff00 100644
--- a/subworkflows/local/baysor_generate_segfree/meta.yml
+++ b/subworkflows/local/baysor_generate_segfree/meta.yml
@@ -22,10 +22,6 @@ output:
       description: |
         loom file generated with the baysor segfree command
         Structure: [ val(meta), path("path-to-ncvs.loom") ]
-  - versions:
-      description: |
-        Files containing software versions
-        Structure: [ path(versions.yml) ]
 authors:
   - "@khersameesh24"
 maintainers:
diff --git a/subworkflows/local/baysor_run_prior_segmentation_mask/meta.yml b/subworkflows/local/baysor_run_prior_segmentation_mask/meta.yml
index 0ce3b51c..f01f44c7 100644
--- a/subworkflows/local/baysor_run_prior_segmentation_mask/meta.yml
+++ b/subworkflows/local/baysor_run_prior_segmentation_mask/meta.yml
@@ -52,10 +52,6 @@ output:
       description: |
         the redefined xenium bundle generated with the segmentation results from baysor
         Structure: [ val(meta), ["redefined-xenium-bundle"] ]
-  - versions:
-      description: |
-        Files containing software versions
-        Structure: [ path(versions.yml) ]
 authors:
   - "@khersameesh24"
 maintainers:
diff --git a/subworkflows/local/baysor_run_transcripts_parquet/meta.yml b/subworkflows/local/baysor_run_transcripts_parquet/meta.yml
index 839cb2ce..ccc4a816 100644
--- a/subworkflows/local/baysor_run_transcripts_parquet/meta.yml
+++ b/subworkflows/local/baysor_run_transcripts_parquet/meta.yml
@@ -48,10 +48,6 @@ output:
       description: |
         the redefined xenium bundle generated with the segmentation results from baysor
         Structure: [ val(meta), ["redefined-xenium-bundle"] ]
-  - versions:
-      description: |
-        Files containing software versions
-        Structure: [ path(versions.yml) ]
 authors:
   - "@khersameesh24"
 maintainers:
diff --git a/subworkflows/local/cellpose_baysor_import_segmentation/meta.yml b/subworkflows/local/cellpose_baysor_import_segmentation/meta.yml
index 8db892d7..0c18e495 100644
--- a/subworkflows/local/cellpose_baysor_import_segmentation/meta.yml
+++ b/subworkflows/local/cellpose_baysor_import_segmentation/meta.yml
@@ -80,10 +80,6 @@ output:
       description: |
         the redefined xenium bundle generated with the segmentation results from baysor
         Structure: [ val(meta), ["redefined-xenium-bundle"] ]
-  - versions:
-      description: |
-        Files containing software versions
-        Structure: [ path(versions.yml) ]
 authors:
   - "@khersameesh24"
 maintainers:
diff --git a/subworkflows/local/cellpose_resolift_morphology_ome_tif/meta.yml b/subworkflows/local/cellpose_resolift_morphology_ome_tif/meta.yml
index 9dfdc52d..b0c99c85 100644
--- a/subworkflows/local/cellpose_resolift_morphology_ome_tif/meta.yml
+++ b/subworkflows/local/cellpose_resolift_morphology_ome_tif/meta.yml
@@ -53,10 +53,6 @@ output:
       description: |
         the redefined xenium bundle generated with the segmentation results from baysor
         Structure: [ val(meta), ["redefined-xenium-bundle"] ]
-  - versions:
-      description: |
-        Files containing software versions
-        Structure: [ path(versions.yml) ]
 authors:
   - "@khersameesh24"
 maintainers:
diff --git a/subworkflows/local/ficture_preprocess_model/meta.yml b/subworkflows/local/ficture_preprocess_model/meta.yml
index 0a970613..17840559 100644
--- a/subworkflows/local/ficture_preprocess_model/meta.yml
+++ b/subworkflows/local/ficture_preprocess_model/meta.yml
@@ -28,10 +28,6 @@ output:
       description: xyz
   - results:
       description: xyz
-  - versions:
-      description: |
-        Files containing software versions
-        Structure: [ path(versions.yml) ]
 authors:
   - "@khersameesh24"
 maintainers:
diff --git a/subworkflows/local/opt_flip_track_stat/meta.yml b/subworkflows/local/opt_flip_track_stat/meta.yml
index 07ccc8b7..ea17599b 100644
--- a/subworkflows/local/opt_flip_track_stat/meta.yml
+++ b/subworkflows/local/opt_flip_track_stat/meta.yml
@@ -39,12 +39,6 @@ output:
         Groovy Map containing summary of the forward oriented probes generated with the panel sequences opt flip and track
         Structure: [ val(meta), path("collapsed_summary.tsv") ]
       pattern: "*.tsv"
-  - versions:
-      type: file
-      description: |
-        File containing software versions
-        Structure: [ path(versions.yml) ]
-      pattern: "versions.yml"
 authors:
   - "@khersameesh24"
 maintainers:
diff --git a/subworkflows/local/proseg_preset_proseg2baysor/meta.yml b/subworkflows/local/proseg_preset_proseg2baysor/meta.yml
index ec8ffbbb..6eb3f091 100644
--- a/subworkflows/local/proseg_preset_proseg2baysor/meta.yml
+++ b/subworkflows/local/proseg_preset_proseg2baysor/meta.yml
@@ -42,10 +42,6 @@ output:
       description: |
         the redefined xenium bundle generated with the segmentation results from baysor
         Structure: [ val(meta), ["redefined-xenium-bundle"] ]
-  - versions:
-      description: |
-        Files containing software versions
-        Structure: [ path(versions.yml) ]
 authors:
   - "@khersameesh24"
 maintainers:
diff --git a/subworkflows/local/segger_create_train_predict/meta.yml b/subworkflows/local/segger_create_train_predict/meta.yml
index 7db69d19..34d59770 100644
--- a/subworkflows/local/segger_create_train_predict/meta.yml
+++ b/subworkflows/local/segger_create_train_predict/meta.yml
@@ -49,10 +49,6 @@ output:
       description: |
         the redefined xenium bundle generated with the segmentation results from baysor
         Structure: [ val(meta), ["redefined-xenium-bundle"] ]
-  - versions:
-      description: |
-        Files containing software versions
-        Structure: [ path(versions.yml) ]
 authors:
   - "@khersameesh24"
 maintainers:
diff --git a/subworkflows/local/spatialdata_write_meta_merge/meta.yml b/subworkflows/local/spatialdata_write_meta_merge/meta.yml
index f8bfa2c4..0168d010 100644
--- a/subworkflows/local/spatialdata_write_meta_merge/meta.yml
+++ b/subworkflows/local/spatialdata_write_meta_merge/meta.yml
@@ -44,10 +44,6 @@ output:
       description: |
         spatialdata object containing the metadata info.
         Structure: [ path(transcripts.parquet) ]
-  - versions:
-      description: |
-        Files containing software versions
-        Structure: [ path(versions.yml) ]
 authors:
   - "@khersameesh24"
 maintainers:
diff --git a/subworkflows/local/xeniumranger_import_segmentation_redefine_bundle/meta.yml b/subworkflows/local/xeniumranger_import_segmentation_redefine_bundle/meta.yml
index a4be036f..fb040abc 100644
--- a/subworkflows/local/xeniumranger_import_segmentation_redefine_bundle/meta.yml
+++ b/subworkflows/local/xeniumranger_import_segmentation_redefine_bundle/meta.yml
@@ -26,10 +26,6 @@ output:
       description: |
         the coordinate space in which xeniumranger import-segmentation was run
         Structure: [ val("microns") ]
-  - versions:
-      description: |
-        Files containing software versions
-        Structure: [ path(versions.yml) ]
 authors:
   - "@khersameesh24"
 maintainers:
diff --git a/subworkflows/local/xeniumranger_relabel_resegment/meta.yml b/subworkflows/local/xeniumranger_relabel_resegment/meta.yml
index d8628f4d..5195335e 100644
--- a/subworkflows/local/xeniumranger_relabel_resegment/meta.yml
+++ b/subworkflows/local/xeniumranger_relabel_resegment/meta.yml
@@ -27,10 +27,6 @@ output:
       description: |
         the redefined xenium bundle generated with the segmentation results from baysor
         Structure: [ val(meta), ["redefined-xenium-bundle"] ]
-  - versions:
-      description: |
-        Files containing software versions
-        Structure: [ path(versions.yml) ]
 authors:
   - "@khersameesh24"
 maintainers:

From cc43da4fcab9d531efa40056328d09adbab8f8f5 Mon Sep 17 00:00:00 2001
From: f641l <florian.heyl@dkfz-heidelberg.de>
Date: Wed, 17 Jun 2026 13:56:22 +0200
Subject: [PATCH 6/8] correction to meta.yml and updating snapshot

---
 modules/local/baysor/create_dataset/meta.yml  | 14 +++++-
 .../baysor/create_dataset/tests/main.nf.test  |  4 +-
 .../create_dataset/tests/main.nf.test.snap    | 24 ++++++++--
 modules/local/baysor/preprocess/meta.yml      | 32 ++++++++++---
 modules/local/baysor/preview/meta.yml         | 46 +++++++++++++------
 modules/local/baysor/run/meta.yml             | 13 +++++-
 modules/local/baysor/segfree/meta.yml         | 39 +++++++++-------
 modules/local/ficture/model/meta.yml          | 26 +++++++++--
 modules/local/ficture/preprocess/meta.yml     | 44 ++++++++++++------
 modules/local/proseg/proseg2baysor/meta.yml   | 45 ++++++++++++------
 modules/local/resolift/meta.yml               | 31 +++++++++----
 modules/local/segger/create_dataset/meta.yml  | 29 ++++++++----
 modules/local/segger/predict/meta.yml         | 39 ++++++++++++----
 modules/local/segger/train/meta.yml           | 29 ++++++++----
 14 files changed, 299 insertions(+), 116 deletions(-)

diff --git a/modules/local/baysor/create_dataset/meta.yml b/modules/local/baysor/create_dataset/meta.yml
index c5091da2..f520c92b 100644
--- a/modules/local/baysor/create_dataset/meta.yml
+++ b/modules/local/baysor/create_dataset/meta.yml
@@ -53,8 +53,6 @@ output:
           description: Subsampled transcripts CSV used as Baysor input dataset.
           pattern: "*/sampled_transcripts.csv"
           ontologies: []
-
-topics:
   versions_baysor:
     - - ${task.process}:
           type: string
@@ -66,6 +64,18 @@ topics:
           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
+      - 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:
   - "@khersameesh24"
 maintainers:
diff --git a/modules/local/baysor/create_dataset/tests/main.nf.test b/modules/local/baysor/create_dataset/tests/main.nf.test
index 41b2742a..e5fc8214 100644
--- a/modules/local/baysor/create_dataset/tests/main.nf.test
+++ b/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") }
             )
         }
     }
diff --git a/modules/local/baysor/create_dataset/tests/main.nf.test.snap b/modules/local/baysor/create_dataset/tests/main.nf.test.snap
index 2a585c4d..1fb129a3 100644
--- a/modules/local/baysor/create_dataset/tests/main.nf.test.snap
+++ b/modules/local/baysor/create_dataset/tests/main.nf.test.snap
@@ -1,15 +1,31 @@
 {
     "versions_stub": {
-        "content": null,
-        "timestamp": "2026-06-17T10:57:59.488545662",
+        "content": [
+            [
+                [
+                    "BAYSOR_CREATE_DATASET",
+                    "baysor",
+                    "0.7.1"
+                ]
+            ]
+        ],
+        "timestamp": "2026-06-17T13:16:19.929465332",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.2"
         }
     },
     "versions": {
-        "content": null,
-        "timestamp": "2026-06-17T10:57:49.73564258",
+        "content": [
+            [
+                [
+                    "BAYSOR_CREATE_DATASET",
+                    "baysor",
+                    "0.7.1"
+                ]
+            ]
+        ],
+        "timestamp": "2026-06-17T13:16:11.036406226",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.2"
diff --git a/modules/local/baysor/preprocess/meta.yml b/modules/local/baysor/preprocess/meta.yml
index a6fc27d0..0bff8178 100644
--- a/modules/local/baysor/preprocess/meta.yml
+++ b/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"
diff --git a/modules/local/baysor/preview/meta.yml b/modules/local/baysor/preview/meta.yml
index 60596066..775e2475 100644
--- a/modules/local/baysor/preview/meta.yml
+++ b/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":
-        type: file
-        description: segmentation preview
-        pattern: "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"
diff --git a/modules/local/baysor/run/meta.yml b/modules/local/baysor/run/meta.yml
index 584c40d9..6856d64a 100644
--- a/modules/local/baysor/run/meta.yml
+++ b/modules/local/baysor/run/meta.yml
@@ -75,8 +75,19 @@ output:
       Statistics of segmented cells
     pattern: "segmentation_cell_stats.csv"
 
+  - 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_baysor:
+  versions:
     - - ${task.process}:
           type: string
           description: The process the versions were collected from
diff --git a/modules/local/baysor/segfree/meta.yml b/modules/local/baysor/segfree/meta.yml
index 8d4e93f9..b64a597c 100644
--- a/modules/local/baysor/segfree/meta.yml
+++ b/modules/local/baysor/segfree/meta.yml
@@ -32,25 +32,32 @@ input:
 
 ## neighborhood composition vectors
 output:
-  - preview_html:
-      - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test' ]
-      - "ncvs.loom":
-        type: file
-        description: loom file with neighborhood results
-        pattern: "ncvs.loom"
+  ncvs:
+    - - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+    - "${prefix}/ncvs.loom":
+      type: file
+      description: |
+        Segmenation file in loom format
+      pattern: "${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_baysor:
+  versions:
     - - ${task.process}:
           type: string
           description: The process the versions were collected from
diff --git a/modules/local/ficture/model/meta.yml b/modules/local/ficture/model/meta.yml
index edde1c11..c957639e 100644
--- a/modules/local/ficture/model/meta.yml
+++ b/modules/local/ficture/model/meta.yml
@@ -32,11 +32,16 @@ input:
         type: file
         description: Another file contains the (unique) names of genes that should be used in analysis. The required columns is just gene (including the header), the naming of genes should match the gene column in the transcript file. If your data contain negative control probes or if you would like to remove certain genes this is where you can specify.
 output:
-  - results:
-      type: file
-      description: Files containing the results of FICTURE
-      pattern: "${meta.id}/results/*"
-topics:
+  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
@@ -47,6 +52,17 @@ topics:
       - "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"
diff --git a/modules/local/ficture/preprocess/meta.yml b/modules/local/ficture/preprocess/meta.yml
index c8eefcba..983125fa 100644
--- a/modules/local/ficture/preprocess/meta.yml
+++ b/modules/local/ficture/preprocess/meta.yml
@@ -30,19 +30,26 @@ input:
         type: file
         description: Another txt file that contains the (unique) names of genes that should be used in analysis. If your data contain negative control probes or if you would like to remove certain genes this is where you can specify. Just list the genes. One gene per line. No header.
 output:
-  - transcripts:
-      type: file
-      description: Transcirpt file used for FICTURE
-      pattern: "processed_transcripts.tsv.gz"
-  - coordinate_minmax:
-      type: file
-      description: Listing the min and max of the coordinates used for FICTURE
-      pattern: "coordinate_minmax.tsv"
-  - features:
-      type: file
-      description: Another file contains the (unique) names of genes that should be used for FICUTRE
-      pattern: "feature.clean.tsv.gz"
-topics:
+  transcripts:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing run information
+            e.g. [id:'sample']
+    - "*processed_transcripts.tsv.gz":
+          type: file
+          description: Transcirpt file used for FICTURE
+          pattern: "processed_transcripts.tsv.gz"
+  coordinate_minmax:
+    - "*coordinate_minmax.tsv":
+          type: file
+          description: Listing the min and max of the coordinates used for FICTURE
+          pattern: "coordinate_minmax.tsv"
+  features:
+    - "*feature.clean.tsv.gz":
+          type: file
+          description: Another file contains the (unique) names of genes that should be used for FICUTRE
+          pattern: "feature.clean.tsv.gz"
   versions_ficture:
     - - ${task.process}:
           type: string
@@ -53,6 +60,17 @@ topics:
       - "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"
diff --git a/modules/local/proseg/proseg2baysor/meta.yml b/modules/local/proseg/proseg2baysor/meta.yml
index 8659b399..440d6914 100644
--- a/modules/local/proseg/proseg2baysor/meta.yml
+++ b/modules/local/proseg/proseg2baysor/meta.yml
@@ -32,20 +32,26 @@ input:
           Transcript metadata file output file from the proseg xenium (format) run
         pattern: "transcript-metadata.csv.gz"
 output:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing run information
-          e.g. `[ id:'run_id']`
-    - xr_polygons:
-        type: file
-        description: 2D polygons for each cell in GeoJSON format. These are flattened from 3D
-        pattern: "xr-cell-polygons.geojson"
-  - - xr_metadata:
-        type: file
-        description: Transcript ids, genes, revised positions, assignment probability
-        pattern: "xr-transcript-metadata.csv"
-topics:
+  xr_polygons:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing run information
+            e.g. `[ id:'run_id']`
+      - "${prefix}/cell-polygons.geojson":
+          type: file
+          description: 2D polygons for each cell in GeoJSON format. These are flattened from 3D
+          pattern: "xr-cell-polygons.geojson"
+  xr_metadata:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing run information
+            e.g. `[ id:'run_id']`
+    - "${prefix}/transcript-metadata.csv":
+          type: file
+          description: Transcript ids, genes, revised positions, assignment probability
+          pattern: "xr-transcript-metadata.csv"
   versions_proseg:
     - - ${task.process}:
           type: string
@@ -56,6 +62,17 @@ topics:
       - "proseg --version | sed 's/proseg //'":
           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
+      - "proseg --version | sed 's/proseg //'":
+          type: eval
+          description: The expression to obtain the version of the tool
 
 authors:
   - "@khersameesh24"
diff --git a/modules/local/resolift/meta.yml b/modules/local/resolift/meta.yml
index 2488c24c..c6f3fbb0 100644
--- a/modules/local/resolift/meta.yml
+++ b/modules/local/resolift/meta.yml
@@ -26,16 +26,16 @@ input:
         pattern: ".tiff"
 
 output:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing run information
-          e.g. `[ id:'run_id']`
-    - output:
-        type: file
-        description: Path to save the upscaled TIFF file.
-        pattern: ".tiff"
-topics:
+  enhanced_tiff:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing run information
+            e.g. `[ id:'run_id']`
+      - "${prefix}/morphology.ome.enhanced.tiff":
+          type: file
+          description: Path to save the upscaled TIFF file.
+          pattern: ".tiff"
   versions_resolift:
     - - ${task.process}:
           type: string
@@ -46,6 +46,17 @@ topics:
       - "pip show resolift | 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 resolift | sed -n 's/^Version: //p'":
+          type: eval
+          description: The expression to obtain the version of the tool
 
 authors:
   - "@kubranarci"
diff --git a/modules/local/segger/create_dataset/meta.yml b/modules/local/segger/create_dataset/meta.yml
index 16f1651c..1f948299 100644
--- a/modules/local/segger/create_dataset/meta.yml
+++ b/modules/local/segger/create_dataset/meta.yml
@@ -24,15 +24,15 @@ input:
         description: |
           Directory containing the raw dataset (e.g., transcripts, boundaries).
 output:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. `[ id:'segger_run_id' ]`
-    - datasetdir:
-        description: |
-          Directory to save the processed Segger dataset (in PyTorch Geometric format).
-topics:
+  datasetdir:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'segger_run_id' ]`
+      - "${prefix}/":
+          description: |
+            Directory to save the processed Segger dataset (in PyTorch Geometric format).
   versions_segger:
     - - ${task.process}:
           type: string
@@ -43,6 +43,17 @@ topics:
       - "pip show segger | 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 segger | sed -n 's/^Version: //p'":
+          type: eval
+          description: The expression to obtain the version of the tool
 
 authors:
   - "@tobiaspk"
diff --git a/modules/local/segger/predict/meta.yml b/modules/local/segger/predict/meta.yml
index 085b0a2b..b4a9b049 100644
--- a/modules/local/segger/predict/meta.yml
+++ b/modules/local/segger/predict/meta.yml
@@ -37,15 +37,25 @@ input:
         description: |
           Directory to save the prediction outputs.
 output:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. `[ id:'segger_run_id' ]`
-    - benchmarks_dir:
-        description: |
-          Directory to save the segmentation results, including cell boundaries and associations.
-topics:
+  benchmarks:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'segger_run_id' ]`
+      - "benchmarks_dir":
+          description: |
+            Directory to save the segmentation results, including cell boundaries and associations.
+  transcripts:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'segger_run_id' ]`
+    - "benchmarks_dir/*/segger_transcripts.parquet":
+          type: file
+          description: |
+            Path to the transcripts.parquet file.
   versions_segger:
     - - ${task.process}:
           type: string
@@ -56,6 +66,17 @@ topics:
       - "pip show segger | 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 segger | sed -n 's/^Version: //p'":
+          type: eval
+          description: The expression to obtain the version of the tool
 
 authors:
   - "@tobiaspk"
diff --git a/modules/local/segger/train/meta.yml b/modules/local/segger/train/meta.yml
index d73e9ba2..7127cdeb 100644
--- a/modules/local/segger/train/meta.yml
+++ b/modules/local/segger/train/meta.yml
@@ -25,16 +25,16 @@ input:
         description: |
           Directory to segger created dataset(s).
 output:
-  - - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'segger_run_id' ]`
-    - trained_models:
-        type: directory
+  trained_models:
+    - - meta:
+        type: map
         description: |
-          Directory to save the trained model and checkpoints.
-topics:
+          Groovy Map containing sample information
+          e.g. `[ id:'segger_run_id' ]`
+      - "trained_models":
+          type: directory
+          description: |
+            Directory to save the trained model and checkpoints.
   versions_segger:
     - - ${task.process}:
           type: string
@@ -45,6 +45,17 @@ topics:
       - "pip show segger | 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 segger | sed -n 's/^Version: //p'":
+          type: eval
+          description: The expression to obtain the version of the tool
 
 authors:
   - "@tobiaspk"

From 469cd921cc1f41c469b955d70e9a3d3adfcae341 Mon Sep 17 00:00:00 2001
From: f641l <florian.heyl@dkfz-heidelberg.de>
Date: Wed, 17 Jun 2026 13:58:50 +0200
Subject: [PATCH 7/8] correction to meta.yml and updating snapshot

---
 modules/local/baysor/segfree/meta.yml | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/modules/local/baysor/segfree/meta.yml b/modules/local/baysor/segfree/meta.yml
index b64a597c..e8ccdad2 100644
--- a/modules/local/baysor/segfree/meta.yml
+++ b/modules/local/baysor/segfree/meta.yml
@@ -34,15 +34,15 @@ input:
 output:
   ncvs:
     - - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test' ]
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
     - "${prefix}/ncvs.loom":
-      type: file
-      description: |
-        Segmenation file in loom format
-      pattern: "${prefix}/ncvs.loom"
+        type: file
+        description: |
+          Segmenation file in loom format
+        pattern: "${prefix}/ncvs.loom"
 
   versions_baysor:
     - - ${task.process}:
@@ -55,7 +55,6 @@ output:
           type: eval
           description: The expression to obtain the version of the tool
 
-
 topics:
   versions:
     - - ${task.process}:

From 59acd7b0c85a98672449a8bf25d822b85a8aea5b Mon Sep 17 00:00:00 2001
From: f641l <florian.heyl@dkfz-heidelberg.de>
Date: Wed, 17 Jun 2026 14:00:37 +0200
Subject: [PATCH 8/8] prettier

---
 modules/local/baysor/preview/meta.yml       |  6 +++---
 modules/local/baysor/run/meta.yml           | 18 +++++++++---------
 modules/local/ficture/preprocess/meta.yml   | 18 +++++++++---------
 modules/local/proseg/proseg2baysor/meta.yml |  6 +++---
 modules/local/segger/predict/meta.yml       |  6 +++---
 5 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/modules/local/baysor/preview/meta.yml b/modules/local/baysor/preview/meta.yml
index 775e2475..f23914e7 100644
--- a/modules/local/baysor/preview/meta.yml
+++ b/modules/local/baysor/preview/meta.yml
@@ -38,9 +38,9 @@ output:
             Groovy Map containing sample information
             e.g. [ id:'test' ]
     - "preview.html":
-          type: file
-          description: segmentation preview
-          pattern: "preview.html"
+        type: file
+        description: segmentation preview
+        pattern: "preview.html"
   versions_baysor:
     - - ${task.process}:
           type: string
diff --git a/modules/local/baysor/run/meta.yml b/modules/local/baysor/run/meta.yml
index 6856d64a..1fbdbbaa 100644
--- a/modules/local/baysor/run/meta.yml
+++ b/modules/local/baysor/run/meta.yml
@@ -76,15 +76,15 @@ output:
     pattern: "segmentation_cell_stats.csv"
 
   - 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
+      - - ${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:
diff --git a/modules/local/ficture/preprocess/meta.yml b/modules/local/ficture/preprocess/meta.yml
index 983125fa..4147cc90 100644
--- a/modules/local/ficture/preprocess/meta.yml
+++ b/modules/local/ficture/preprocess/meta.yml
@@ -37,19 +37,19 @@ output:
             Groovy Map containing run information
             e.g. [id:'sample']
     - "*processed_transcripts.tsv.gz":
-          type: file
-          description: Transcirpt file used for FICTURE
-          pattern: "processed_transcripts.tsv.gz"
+        type: file
+        description: Transcirpt file used for FICTURE
+        pattern: "processed_transcripts.tsv.gz"
   coordinate_minmax:
     - "*coordinate_minmax.tsv":
-          type: file
-          description: Listing the min and max of the coordinates used for FICTURE
-          pattern: "coordinate_minmax.tsv"
+        type: file
+        description: Listing the min and max of the coordinates used for FICTURE
+        pattern: "coordinate_minmax.tsv"
   features:
     - "*feature.clean.tsv.gz":
-          type: file
-          description: Another file contains the (unique) names of genes that should be used for FICUTRE
-          pattern: "feature.clean.tsv.gz"
+        type: file
+        description: Another file contains the (unique) names of genes that should be used for FICUTRE
+        pattern: "feature.clean.tsv.gz"
   versions_ficture:
     - - ${task.process}:
           type: string
diff --git a/modules/local/proseg/proseg2baysor/meta.yml b/modules/local/proseg/proseg2baysor/meta.yml
index 440d6914..3d5cfac4 100644
--- a/modules/local/proseg/proseg2baysor/meta.yml
+++ b/modules/local/proseg/proseg2baysor/meta.yml
@@ -49,9 +49,9 @@ output:
             Groovy Map containing run information
             e.g. `[ id:'run_id']`
     - "${prefix}/transcript-metadata.csv":
-          type: file
-          description: Transcript ids, genes, revised positions, assignment probability
-          pattern: "xr-transcript-metadata.csv"
+        type: file
+        description: Transcript ids, genes, revised positions, assignment probability
+        pattern: "xr-transcript-metadata.csv"
   versions_proseg:
     - - ${task.process}:
           type: string
diff --git a/modules/local/segger/predict/meta.yml b/modules/local/segger/predict/meta.yml
index b4a9b049..777f768a 100644
--- a/modules/local/segger/predict/meta.yml
+++ b/modules/local/segger/predict/meta.yml
@@ -53,9 +53,9 @@ output:
             Groovy Map containing sample information
             e.g. `[ id:'segger_run_id' ]`
     - "benchmarks_dir/*/segger_transcripts.parquet":
-          type: file
-          description: |
-            Path to the transcripts.parquet file.
+        type: file
+        description: |
+          Path to the transcripts.parquet file.
   versions_segger:
     - - ${task.process}:
           type: string