Json schema improvements

assets/schema_input.json

@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/fetchngs/master/assets/schema_input.json",
     "title": "nf-core/fetchngs pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",

modules.json

@@ -45,9 +45,9 @@
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     },
-                    "utils_nfvalidation_plugin": {
+                    "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }
                 }

nextflow.config

@@ -45,10 +45,10 @@ params {
     max_time                    = '240.h'
 
     // Schema validation default options
-    validationFailUnrecognisedParams = false
-    validationLenientMode            = false
-    validationShowHiddenParams       = false
-    validationSchemaIgnoreParams     = ''
+    // validationFailUnrecognisedParams = false
+    // validationLenientMode            = false
+    // validationShowHiddenParams       = false
+    // validationSchemaIgnoreParams     = ''
     validate_params                  = true
 
     // Deprecated options
@@ -176,7 +176,7 @@ singularity.registry = 'quay.io'
 
 // Nextflow plugins
 plugins {
-    id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container

nextflow_schema.json

@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/fetchngs/master/nextflow_schema.json",
     "title": "nf-core/fetchngs pipeline parameters",
     "description": "Pipeline to fetch metadata and raw FastQ files from public databases",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -269,19 +269,19 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/institutional_config_options"
+            "$ref": "#/$defs/institutional_config_options"
         },
         {
-            "$ref": "#/definitions/max_job_request_options"
+            "$ref": "#/$defs/max_job_request_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/generic_options"
         },
         {
-            "$ref": "#/definitions/deprecated_options"
+            "$ref": "#/$defs/deprecated_options"
         }
     ]
 }

subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf

@@ -8,9 +8,9 @@
 ========================================================================================
 */
 
-include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
-include { fromSamplesheet           } from 'plugin/nf-validation'
-include { paramsSummaryMap          } from 'plugin/nf-validation'
+include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin'
+include { samplesheetToList           } from 'plugin/nf-schema'
+include { paramsSummaryMap          } from 'plugin/nf-schema'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
@@ -56,13 +56,10 @@ workflow PIPELINE_INITIALISATION {
     pre_help_text = nfCoreLogo(monochrome_logs)
     post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
     def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input ids.csv --outdir <OUTDIR>"
-    UTILS_NFVALIDATION_PLUGIN (
-        help,
-        workflow_command,
-        pre_help_text,
-        post_help_text,
+    UTILS_NFSCHEMA_PLUGIN (
+        workflow,
         validate_params,
-        "nextflow_schema.json"
+        null
     )
 
     //