Update schema to use new definitions groups

Author: ewels

nextflow_schema.json

@@ -4,8 +4,9 @@
     "title": "nf-core/atacseq pipeline parameters",
     "description": "ATACSeq peak-calling and differential analysis pipeline.",
     "type": "object",
-    "properties": {
-        "Input/output options": {
+    "definitions": {
+        "input_output_options": {
+            "title": "Input/output options",
             "type": "object",
             "properties": {
                 "input": {
@@ -53,7 +54,8 @@
             ],
             "fa_icon": "fas fa-terminal"
         },
-        "Reference genome options": {
+        "reference_genome_options": {
+            "title": "Reference genome options",
             "type": "object",
             "properties": {
                 "genome": {
@@ -124,7 +126,8 @@
             },
             "fa_icon": "fas fa-dna"
         },
-        "Adapter trimming options": {
+        "adapter_trimming_options": {
+            "title": "Adapter trimming options",
             "type": "object",
             "properties": {
                 "clip_r1": {
@@ -177,7 +180,8 @@
             },
             "fa_icon": "fas fa-cut"
         },
-        "Alignment options": {
+        "alignment_options": {
+            "title": "Alignment options",
             "type": "object",
             "properties": {
                 "keep_dups": {
@@ -223,7 +227,8 @@
             },
             "fa_icon": "fas fa-map-signs"
         },
-        "Peak calling options": {
+        "peak_calling_options": {
+            "title": "Peak calling options",
             "type": "object",
             "properties": {
                 "narrow_peak": {
@@ -285,7 +290,8 @@
             },
             "fa_icon": "fas fa-chart-area"
         },
-        "Differential analysis options": {
+        "differential_analysis_options": {
+            "title": "Differential analysis options",
             "type": "object",
             "properties": {
                 "deseq2_vst": {
@@ -305,7 +311,8 @@
             },
             "fa_icon": "fas fa-not-equal"
         },
-        "Process skipping options": {
+        "process_skipping_options": {
+            "title": "Process skipping options",
             "type": "object",
             "properties": {
                 "skip_fastqc": {
@@ -359,7 +366,8 @@
             },
             "fa_icon": "fas fa-forward"
         },
-        "Institutional config options": {
+        "institutional_config_options": {
+            "title": "Institutional config options",
             "type": "object",
             "properties": {
                 "custom_config_version": {
@@ -409,7 +417,8 @@
             },
             "fa_icon": "fas fa-university"
         },
-        "Max job request options": {
+        "max_job_request_options": {
+            "title": "Max job request options",
             "type": "object",
             "properties": {
                 "max_cpus": {
@@ -439,7 +448,8 @@
             },
             "fa_icon": "fab fa-acquisitions-incorporated"
         },
-        "Generic options": {
+        "generic_options": {
+            "title": "Generic options",
             "type": "object",
             "properties": {
                 "help": {
@@ -536,5 +546,37 @@
             },
             "fa_icon": "fas fa-file-import"
         }
-    }
-}
+    },
+    "allOf": [
+        {
+            "$ref": "#/definitions/input_output_options"
+        },
+        {
+            "$ref": "#/definitions/reference_genome_options"
+        },
+        {
+            "$ref": "#/definitions/adapter_trimming_options"
+        },
+        {
+            "$ref": "#/definitions/alignment_options"
+        },
+        {
+            "$ref": "#/definitions/peak_calling_options"
+        },
+        {
+            "$ref": "#/definitions/differential_analysis_options"
+        },
+        {
+            "$ref": "#/definitions/process_skipping_options"
+        },
+        {
+            "$ref": "#/definitions/institutional_config_options"
+        },
+        {
+            "$ref": "#/definitions/max_job_request_options"
+        },
+        {
+            "$ref": "#/definitions/generic_options"
+        }
+    ]
+}