Fix broken schema references preventing Seqera Platform launch

README.md

@@ -35,6 +35,8 @@ nextflow run Sage-Bionetworks-Workflows/nf-artist --input <path-to-samplesheet>
 ├── outdir
 │   ├── <simpleName or id for first row of samplesheet>
 │   │   ├── thumbnail.jpeg
+│   │   ├── ometiff (optional, if --save_ometiff is true)
+│   │   │   ├── <image>.ome.tiff
 │   │   ├── minerva
 │   │   │   ├── index.html
 │   │   │   ├── exhibit.json
@@ -56,6 +58,8 @@ nextflow run Sage-Bionetworks-Workflows/nf-artist --input <path-to-samplesheet>
 
 * **outdir**: Specifies the directory where the output data should be saved. Default is "outputs". (Type: String)
 
+* **save_ometiff**: Setting this to true will save converted OME-TIFF files to the output directory in an `ometiff` subdirectory. Default is false. (Type: Boolean)
+
 #### Miniature Options:
 
 * **remove_bg**: Setting this to true will remove the non-tissue background. Default is true. (Type: Boolean)

main.nf

@@ -6,6 +6,7 @@ nextflow.enable.dsl=2
 if (params.input) { params.input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
 
 params.outdir = "outputs"
+params.save_ometiff = false
 params.remove_bg = true
 params.level = -1
 params.dimred = "umap"

modules/bioformats2ometiff.nf

@@ -5,6 +5,10 @@ process bioformats2ometiff {
       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

@@ -22,10 +22,15 @@
                     "type": "string",
                     "description": "Directory in which outputs are placed",
                     "default": "outputs"
+                },
+                "save_ometiff": {
+                    "type": "boolean",
+                    "description": "Save converted OME-TIFF files to output directory",
+                    "default": false
                 }
             }
         },
-        "miniatue_options": {
+        "miniature_options": {
             "title": "Miniature options",
             "type": "object",
             "fa_icon": "fas fa-palette",
@@ -38,7 +43,7 @@
                 },
                 "level": {
                     "type": "integer",
-                    "description": "The pyramid level used in thumbnauls, Default: -1 (smallest)",
+                    "description": "The pyramid level used in thumbnails, Default: -1 (smallest)",
                     "default": -1
                 },
                 "dimred": {
@@ -49,13 +54,13 @@
                 },
                 "colormap": {
                     "type": "string",
-                    "description": "The colormap used. Ensure colormap is compatiable with `n_components` selected ",
+                    "description": "The colormap used. Ensure colormap is compatible with `n_components` selected ",
                     "enum": ["UCIE", "LAB", "RGB", "BREMM", "SCHUMANN", "STEIGER", "TEULING2", "ZIEGLER","CUBEDIAGONAL"],
                     "default": "UCIE"
                 },
                 "n_components": {
                     "type": "integer",
-                    "description": "",
+                    "description": "Number of components for dimensionality reduction",
                     "default": 3,
                     "enum": [2,3]
                 }
@@ -64,7 +69,10 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/parameters"
+            "$ref": "#/definitions/input_output_options"
+        },
+        {
+            "$ref": "#/definitions/miniature_options"
         }
     ]
 }