Move publishDir after output block and fix schema typo

Co-authored-by: adamjtaylor <14945787+adamjtaylor@users.noreply.github.com>

Author: Copilot

modules/bioformats2ometiff.nf

@@ -1,14 +1,14 @@
 process bioformats2ometiff {
   tag {"$meta.id"}
   label "process_medium"
-  publishDir "$params.outdir",
-    enabled: params.save_ometiff,
-    pattern: "*.ome.tiff",
-    saveAs: {filename -> "${meta.id}/ometiff/${filename}"}
   input:
       tuple val(meta), file(image) 
   output:
       tuple val(meta), file("${image.simpleName}.ome.tiff")
+  publishDir "$params.outdir",
+    enabled: params.save_ometiff,
+    pattern: "*.ome.tiff",
+    saveAs: {filename -> "${meta.id}/ometiff/${filename}"}
   stub:
   """
   touch raw_dir

nextflow_schema.json

@@ -30,7 +30,7 @@
                 }
             }
         },
-        "miniatue_options": {
+        "miniature_options": {
             "title": "Miniature options",
             "type": "object",
             "fa_icon": "fas fa-palette",
@@ -72,7 +72,7 @@
             "$ref": "#/definitions/input_output_options"
         },
         {
-            "$ref": "#/definitions/miniatue_options"
+            "$ref": "#/definitions/miniature_options"
         }
     ]
 }