Merge pull request #2 from artic-network/dev

reformat schema

nextflow.config

@@ -63,13 +63,13 @@ params {
 }
 
 manifest {
-    name            = 'epi2me-labs/wf-artic'
-    author          = 'Oxford Nanopore Technologies'
-    homePage        = 'https://github.com/epi2me-labs/wf-artic'
+    name            = 'artic-mpxv-nf'
+    author          = 'Oxford Nanopore Technologies. artic-network: Sam Wilkinson, Rachel Colquhoun'
+    homePage        = 'https://github.com/artic-network/artic-mpxv-nf'
     description     = 'Run the ARTIC SARS-CoV-2 methodology on multiplexed MinION, GridION, and PromethION data.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = 'v1.0.0'
+    version         = 'v1.0.1'
 }
 
 epi2melabs {
@@ -88,9 +88,9 @@ process {
         container = "ontresearch/wf-common:${params.wf.common_sha}"
         memory = '1G'
     }
-    withLabel:artic { 
+    withLabel:artic {
         container = "quay.io/artic/fieldbioinformatics:1.4.0"
-        memory = '2G'    
+        memory = '2G'
     }
     withLabel:pangolin {
         container = "ontresearch/pangolin:${params.wf.pangolin_sha}"

nextflow_schema.json

@@ -41,7 +41,7 @@
           "type": "string",
           "default": "MPXV",
           "description": "Primer scheme name.",
-          "help_text": "This should be set to `SARS-CoV-2`, or `spike-seq` or your custom scheme name. This affects the choice of scheme versions you can use. The only scheme versions compatible with `spike-seq` are `ONT/V1` and `ONT/V4.1`"
+          "help_text": "This should be set to `MPXV`"
         },
         "scheme_version": {
           "type": "string",
@@ -90,6 +90,16 @@
         }
       }
     },
+    "mpxv_options": {
+      "title": "Monkeypox virus Options",
+      "type": "object",
+      "description": "Options related to MPXV",
+      "default": "",
+      "properties": {
+      },
+      "fa_icon": "fas fa-address-card",
+      "help_text": ""
+    },
     "advanced_options": {
       "title": "Advanced Options",
       "type": "object",
@@ -223,6 +233,9 @@
     {
       "$ref": "#/definitions/output"
     },
+    {
+      "$ref": "#/definitions/mpxv_options"
+    },
     {
       "$ref": "#/definitions/advanced_options"
     },