Add parameter to skip SpatialData merging

Add a parameter to skip aggregation of per-sample SpatialData objects into one, which is set to `false` by default.
nf-core · Nov 8, 2024 · 9e25800 · 9e25800
1 parent 846bdff
commit 9e25800
Show file tree

Hide file tree

Showing 3 changed files with 24 additions and 0 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -97,4 +97,8 @@ process {
         ]
     }
 
+    withName: 'MERGE_SDATA' {
+        ext.when = params.merge_sdata
+    }
+
 }
diff --git a/nextflow.config b/nextflow.config
@@ -33,6 +33,9 @@ params {
     svg_autocorr_method       = "moran"
     n_top_svgs                = 14
 
+    // Data aggregation
+    merge_sdata                  = false
+
     // MultiQC options
     multiqc_config               = null
     multiqc_title                = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -164,6 +164,20 @@
             }
         },
 
+        "aggregation_options": {
+            "title": "Data aggregation options",
+            "type": "object",
+            "fa_icon": "fas fa-rocket",
+            "description": "Options related to aggregation of final data objects",
+            "properties": {
+                "merge_sdata": {
+                    "type": "boolean",
+                    "description": "Merge per-sample SpatialData objects into one",
+                    "fa_icon": "fas fa-arrows-to-dot"
+                }
+            }
+        },
+
         "institutional_config_options": {
             "title": "Institutional config options",
             "type": "object",
@@ -317,6 +331,9 @@
         {
             "$ref": "#/$defs/analysis_options"
         },
+        {
+            "$ref": "#/$defs/aggregation_options"
+        },
         {
             "$ref": "#/$defs/institutional_config_options"
         },