Merge pull request #133 from nf-core/132-json-schema-nanostring

JSON schema

Author: apeltzer

CHANGELOG.md

@@ -11,8 +11,7 @@ Initial release of nf-core/nanostring, created with the [nf-core](https://nf-co.
 
 ### `Fixed`
 
-### `Changed`
-
+- [#133](https://github.com/nf-core/nanostring/pull/133/) - Improvements to JSON schema and minor linting changes
 - [#136](https://github.com/nf-core/nanostring/pull/136) - Replaced `NORMALIZE` and `QUALITY_CONTROL` for its modules.
 
 ### `Dependencies`

nextflow_schema.json

@@ -28,18 +28,6 @@
                     "format": "directory-path",
                     "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                     "fa_icon": "fas fa-folder-open"
-                },
-                "email": {
-                    "type": "string",
-                    "description": "Email address for completion summary.",
-                    "fa_icon": "fas fa-envelope",
-                    "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
-                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
-                },
-                "multiqc_title": {
-                    "type": "string",
-                    "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
-                    "fa_icon": "fas fa-file-signature"
                 }
             }
         },
@@ -71,6 +59,7 @@
                 "normalization_method": {
                     "type": "string",
                     "default": "GEO",
+                    "enum": ["GEO", "GLM"],
                     "fa_icon": "fas fa-compress-arrows-alt",
                     "description": "The method to use for normalization of nCounter data.",
                     "help_text": "Available options are `GEO` (default) or `GLM`."
@@ -91,7 +80,7 @@
                     "description": "This selects the algorithm for computing the respective gene score. Default is 'plage.dir'."
                 },
                 "gene_score_yaml": {
-                    "type": "string",
+                    "format": "file-path",
                     "fa_icon": "fas fa-align-justify",
                     "help_text": "The YAML format is as such:\n\n```\nscore_name: \n    - GENE1\n    - GENE2\n    - GENE3\n```",
                     "description": "This sets the YAML to be used for computing the gene scores. Needs both a name for each set of genes and respective genes to be selected."
@@ -209,6 +198,13 @@
                     "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
                     "hidden": true
                 },
+                "email": {
+                    "type": "string",
+                    "description": "Email address for completion summary.",
+                    "fa_icon": "fas fa-envelope",
+                    "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
+                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
+                },
                 "email_on_fail": {
                     "type": "string",
                     "description": "Email address for completion summary, only when pipeline fails.",
@@ -244,6 +240,11 @@
                     "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
                     "hidden": true
                 },
+                "multiqc_title": {
+                    "type": "string",
+                    "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
+                    "fa_icon": "fas fa-file-signature"
+                },
                 "multiqc_config": {
                     "type": "string",
                     "format": "file-path",