From 9e25800c7d18add8a47d30ce1b6c5609ed797ec9 Mon Sep 17 00:00:00 2001
From: Erik Fasterius <erik.fasterius@outlook.com>
Date: Fri, 8 Nov 2024 17:02:46 +0100
Subject: [PATCH] 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.
---
 conf/modules.config  |  4 ++++
 nextflow.config      |  3 +++
 nextflow_schema.json | 17 +++++++++++++++++
 3 files changed, 24 insertions(+)

diff --git a/conf/modules.config b/conf/modules.config
index 9cb5c54..deee170 100644
--- 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
index 076e3bb..5669206 100644
--- 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
index 9f34778..5d05296 100644
--- 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"
         },