fix: apply topic channels and update meta.yml structure for xeniumranger

an-altosian · an-altosian · commit 72a66233bf6d · 2025-12-08T18:16:17.000Z
diff --git a/modules/nf-core/xeniumranger/import-segmentation/main.nf b/modules/nf-core/xeniumranger/import-segmentation/main.nf
@@ -5,17 +5,11 @@ process XENIUMRANGER_IMPORT_SEGMENTATION {
     container "nf-core/xeniumranger:4.0"
 
     input:
-    tuple val(meta),
-          path(xenium_bundle, stageAs: "bundle/"),
-          path(transcript_assignment),
-          path(viz_polygons),
-          path(nuclei),
-          path(cells),
-          path(coordinate_transform)
-    
+    tuple val(meta), path(xenium_bundle, stageAs: "bundle/"), path(transcript_assignment), path(viz_polygons), path(nuclei), path(cells), path(coordinate_transform)
+
     output:
     tuple val(meta), path("${prefix}"), emit: outs
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val("xeniumranger"), eval("xeniumranger -V | sed -e 's/xeniumranger-/- /g'"), emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -46,11 +40,6 @@ process XENIUMRANGER_IMPORT_SEGMENTATION {
         --localcores=${task.cpus} \\
         --localmem=${task.memory.toGiga()} \\
         ${args}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g")
-    END_VERSIONS
     """
 
     stub:
@@ -84,10 +73,5 @@ process XENIUMRANGER_IMPORT_SEGMENTATION {
         mkdir -p "${prefix}"
         touch "${prefix}/dry_run.txt"
     fi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/xeniumranger/import-segmentation/meta.yml b/modules/nf-core/xeniumranger/import-segmentation/meta.yml
@@ -1,9 +1,9 @@
 name: xeniumranger_import_segmentation
-description: The xeniumranger import-segmentation module allows you to specify 2D
-  nuclei and/or cell segmentation results for assigning transcripts to cells and recalculate
-  all Xenium Onboard Analysis (XOA) outputs that depend on segmentation. Segmentation
-  results can be generated by community-developed tools or prior Xenium segmentation
-  result.
+description: The xeniumranger import-segmentation module allows you to specify
+  2D nuclei and/or cell segmentation results for assigning transcripts to cells
+  and recalculate all Xenium Onboard Analysis (XOA) outputs that depend on
+  segmentation. Segmentation results can be generated by community-developed
+  tools or prior Xenium segmentation result.
 keywords:
   - spatial
   - segmentation
@@ -31,44 +31,70 @@ input:
           e.g. [id:'xenium_sample']
     - xenium_bundle:
         type: directory
-        description: Path to the Xenium output bundle generated by the Xenium Onboard Analysis pipeline
-    - nuclei:
+        description: Path to the Xenium output bundle generated by the Xenium
+          Onboard Analysis pipeline
+    - transcript_assignment:
         type: file
         optional: true
-        description: Optional nucleus segmentation input passed to `--nuclei`
-    - cells:
+        description: Optional transcript assignment CSV passed to
+          `--transcript-assignment`
+        ontologies: []
+    - viz_polygons:
         type: file
         optional: true
-        description: Optional cell segmentation input passed to `--cells`
-    - transcript_assignment:
+        description: Optional visualization polygons GeoJSON passed to
+          `--viz-polygons`
+        ontologies: []
+    - nuclei:
         type: file
         optional: true
-        description: Optional transcript assignment CSV passed to `--transcript-assignment`
-    - viz_polygons:
+        description: Optional nucleus segmentation input passed to `--nuclei`
+        ontologies: []
+    - cells:
         type: file
         optional: true
-        description: Optional visualization polygons GeoJSON passed to `--viz-polygons`
+        description: Optional cell segmentation input passed to `--cells`
+        ontologies: []
     - coordinate_transform:
         type: file
         optional: true
-        description: Optional image alignment transform passed to `--coordinate-transform`
+        description: Optional image alignment transform passed to
+          `--coordinate-transform`
+        ontologies: []
 output:
   outs:
-    - meta:
-        type: map
-        description: Groovy Map containing sample information e.g. [ id:'test' ]
-    - "${meta.id}":
-        type: directory
-        description: Directory containing the output xenium bundle of Xenium Ranger
-        pattern: "${meta.id}"
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information e.g. [ id:'test' ]
+      - "${prefix}":
+          type: directory
+          description: Directory containing the output xenium bundle of Xenium
+            Ranger
+          pattern: "${prefix}"
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - "${task.process}":
+          type: string
+          description: The process the versions were collected from
+      - xeniumranger:
+          type: string
+          description: The tool name
+      - "xeniumranger -V | sed -e 's/xeniumranger-/- /g'":
+          type: string
+          description: The command used to generate the version of the tool
+topics:
+  versions:
+    - - "${task.process}":
+          type: string
+          description: The process the versions were collected from
+      - xeniumranger:
+          type: string
+          description: The tool name
+      - "xeniumranger -V | sed -e 's/xeniumranger-/- /g'":
+          type: string
+          description: The command used to generate the version of the tool
 authors:
   - "@khersameesh24"
+  - "@an-altosian"
 maintainers:
   - "@khersameesh24"
+  - "@an-altosian"
diff --git a/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test b/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test
@@ -13,7 +13,7 @@ nextflow_process {
 
     setup {
         run("UNTAR") {
-            script "../../../untar/main.nf"
+            script "modules/nf-core/untar/main.nf"
             process {
                 """
                 input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/xenium_bundle.tar.gz', checkIfExists: true)]
diff --git a/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test.snap b/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test.snap
@@ -13,7 +13,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,773a1ba600c527d6b9b3d62faf58d4bc"
+                    [
+                        "XENIUMRANGER_IMPORT_SEGMENTATION",
+                        "xeniumranger",
+                        "xeniumranger xenium-4.0.1.1"
+                    ]
                 ],
                 "outs": [
                     [
@@ -26,14 +30,18 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,773a1ba600c527d6b9b3d62faf58d4bc"
+                    [
+                        "XENIUMRANGER_IMPORT_SEGMENTATION",
+                        "xeniumranger",
+                        "xeniumranger xenium-4.0.1.1"
+                    ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.2"
         },
-        "timestamp": "2025-12-05T05:33:33.73241842"
+        "timestamp": "2025-12-08T18:09:01.800602245"
     }
 }
diff --git a/modules/nf-core/xeniumranger/relabel/tests/main.nf.test b/modules/nf-core/xeniumranger/relabel/tests/main.nf.test
@@ -13,7 +13,7 @@ nextflow_process {
 
     setup {
             run("UNTAR") {
-                script "../../../untar/main.nf"
+                script "modules/nf-core/untar/main.nf"
                 process {
                     """
                     input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/xenium_bundle.tar.gz', checkIfExists: true)]
diff --git a/modules/nf-core/xeniumranger/rename/tests/main.nf.test b/modules/nf-core/xeniumranger/rename/tests/main.nf.test
@@ -13,7 +13,7 @@ nextflow_process {
 
     setup {
             run("UNTAR") {
-                script "../../../untar/main.nf"
+                script "modules/nf-core/untar/main.nf"
                 process {
                     """
                     input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/xenium_bundle.tar.gz', checkIfExists: true)]
diff --git a/modules/nf-core/xeniumranger/resegment/tests/main.nf.test b/modules/nf-core/xeniumranger/resegment/tests/main.nf.test
@@ -13,7 +13,7 @@ nextflow_process {
 
     setup {
             run("UNTAR") {
-                script "../../../untar/main.nf"
+                script "modules/nf-core/untar/main.nf"
                 process {
                     """
                     input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/xenium_bundle.tar.gz', checkIfExists: true)]
diff --git a/subworkflows/nf-core/xeniumranger/import_segmentation_image/main.nf b/subworkflows/nf-core/xeniumranger/import_segmentation_image/main.nf
@@ -9,7 +9,6 @@ workflow XENIUMRANGER_IMPORT_SEGMENTATION_IMAGE {
     ch_coordinate_transform    // [meta, coordinate_transform] (use [] if absent)
 
     main:
-    ch_versions = channel.empty()
 
     def input = ch_bundle
         .map { meta, bundle -> [meta.id, [meta, bundle]] }
@@ -50,9 +49,8 @@ workflow XENIUMRANGER_IMPORT_SEGMENTATION_IMAGE {
         }
 
     XENIUMRANGER_IMPORT_SEGMENTATION(input)
-    ch_versions = ch_versions.mix(XENIUMRANGER_IMPORT_SEGMENTATION.out.versions)
 
     emit:
     outs     = XENIUMRANGER_IMPORT_SEGMENTATION.out.outs
-    versions = ch_versions
+    versions = XENIUMRANGER_IMPORT_SEGMENTATION.out.versions
 }
diff --git a/subworkflows/nf-core/xeniumranger/import_segmentation_image/meta.yml b/subworkflows/nf-core/xeniumranger/import_segmentation_image/meta.yml
@@ -7,8 +7,9 @@ keywords:
   - import segmentation
   - nuclei
   - cells
-modules:
+components:
   - xeniumranger/import-segmentation
+  - xeniumranger/import/segmentation
 input:
   - ch_input:
       description: >
@@ -34,21 +35,22 @@ input:
             optional: true
             description: Optional image alignment transform CSV. Use [] if absent.
 output:
-  outs:
-    description: Channel of Xenium bundle outputs produced by import-segmentation
-    structure:
-      - meta:
-          type: map
-          description: Sample metadata
-      - "${meta.id}":
-          type: directory
-          description: Output Xenium bundle directory
-  versions:
-    description: Aggregated versions emitted by the module
-    structure:
-      - path:
-          type: file
-          description: `versions.yml`
+  - outs:
+      description: Channel of Xenium bundle outputs produced by import-segmentation
+      structure:
+        - meta:
+            type: map
+            description: Sample metadata
+        - "${meta.id}":
+            type: directory
+            description: Output Xenium bundle directory
+  - versions:
+      description: Aggregated versions emitted by the module
+      structure:
+        - path:
+            type: file
+            description: "versions.yml"
+authors:
+  - "@an-altosian"
 maintainers:
-  - "@your_github_handle"
-
+  - "@an-altosian"
diff --git a/subworkflows/nf-core/xeniumranger/import_segmentation_image/tests/main.nf.test b/subworkflows/nf-core/xeniumranger/import_segmentation_image/tests/main.nf.test
@@ -7,10 +7,11 @@ nextflow_workflow {
 
     tag "subworkflows"
     tag "subworkflows_nfcore"
+    tag "subworkflows/xeniumranger/import_segmentation_image"
     tag "xeniumranger"
     tag "xeniumranger/import_segmentation_image"
     tag "untar"
-    tag "xeniumranger/import_segmentation"
+    tag "xeniumranger/import-segmentation"
 
     setup {
         run("UNTAR") {
diff --git a/subworkflows/nf-core/xeniumranger/import_segmentation_image/tests/main.nf.test.snap b/subworkflows/nf-core/xeniumranger/import_segmentation_image/tests/main.nf.test.snap
diff --git a/subworkflows/nf-core/xeniumranger/import_segmentation_transcript/main.nf b/subworkflows/nf-core/xeniumranger/import_segmentation_transcript/main.nf
diff --git a/subworkflows/nf-core/xeniumranger/import_segmentation_transcript/meta.yml b/subworkflows/nf-core/xeniumranger/import_segmentation_transcript/meta.yml
diff --git a/subworkflows/nf-core/xeniumranger/import_segmentation_transcript/tests/main.nf.test b/subworkflows/nf-core/xeniumranger/import_segmentation_transcript/tests/main.nf.test

Original file line number	Diff line number	Diff line change
`@@ -13,7 +13,11 @@`
`13`	`13`	`]`
`14`	`14`	`],`
`15`	`15`	`"1": [`
`16`		`- "versions.yml:md5,773a1ba600c527d6b9b3d62faf58d4bc"`
	`16`	`+ [`
	`17`	`+ "XENIUMRANGER_IMPORT_SEGMENTATION",`
	`18`	`+ "xeniumranger",`
	`19`	`+ "xeniumranger xenium-4.0.1.1"`
	`20`	`+ ]`
`17`	`21`	`],`
`18`	`22`	`"outs": [`
`19`	`23`	`[`
`@@ -26,14 +30,18 @@`
`26`	`30`	`]`
`27`	`31`	`],`
`28`	`32`	`"versions": [`
`29`		`- "versions.yml:md5,773a1ba600c527d6b9b3d62faf58d4bc"`
	`33`	`+ [`
	`34`	`+ "XENIUMRANGER_IMPORT_SEGMENTATION",`
	`35`	`+ "xeniumranger",`
	`36`	`+ "xeniumranger xenium-4.0.1.1"`
	`37`	`+ ]`
`30`	`38`	`]`
`31`	`39`	`}`
`32`	`40`	`],`
`33`	`41`	`"meta": {`
`34`	`42`	`"nf-test": "0.9.3",`
`35`	`43`	`"nextflow": "25.04.2"`
`36`	`44`	`},`
`37`		`- "timestamp": "2025-12-05T05:33:33.73241842"`
	`45`	`+ "timestamp": "2025-12-08T18:09:01.800602245"`
`38`	`46`	`}`
`39`	`47`	`}`
Original file line number	Diff line number	Diff line change
`@@ -9,7 +9,6 @@ workflow XENIUMRANGER_IMPORT_SEGMENTATION_IMAGE {`
`9`	`9`	`ch_coordinate_transform // [meta, coordinate_transform] (use [] if absent)`
`10`	`10`
`11`	`11`	`main:`
`12`		`- ch_versions = channel.empty()`
`13`	`12`
`14`	`13`	`def input = ch_bundle`
`15`	`14`	`.map { meta, bundle -> [meta.id, [meta, bundle]] }`
`@@ -50,9 +49,8 @@ workflow XENIUMRANGER_IMPORT_SEGMENTATION_IMAGE {`
`50`	`49`	`}`
`51`	`50`
`52`	`51`	`XENIUMRANGER_IMPORT_SEGMENTATION(input)`
`53`		`- ch_versions = ch_versions.mix(XENIUMRANGER_IMPORT_SEGMENTATION.out.versions)`
`54`	`52`
`55`	`53`	`emit:`
`56`	`54`	`outs = XENIUMRANGER_IMPORT_SEGMENTATION.out.outs`
`57`		`- versions = ch_versions`
	`55`	`+ versions = XENIUMRANGER_IMPORT_SEGMENTATION.out.versions`
`58`	`56`	`}`