start updating json schema

assets/schema_input.json

@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft//sch2020-12ema",
     "$id": "https://raw.githubusercontent.com/nf-core/cutandrun/master/assets/schema_input.json",
     "title": "nf-core/cutandrun pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",

main.nf

@@ -40,16 +40,16 @@ if(params.normalisation_mode == "Spikein") {
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { validateParameters; paramsHelp } from 'plugin/nf-validation'
+include { validateParameters; paramsHelp } from 'plugin/nf-schema'
 
 // Print help message if needed
-if (params.help) {
-    def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
-    def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-    def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
-    log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
-    System.exit(0)
-}
+// if (params.help) {
+    // def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
+    // def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
+    // def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
+    // log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
+    // System.exit(0)
+// }
 
 // Validate input parameters
 if (params.validate_params) {

nextflow.config

@@ -79,13 +79,13 @@ params {
     seacr_peak_threshold       = 0.05
     macs2_pvalue               = null
     macs2_qvalue               = 0.01
-    macs_gsize                 = 2700000000.0
+    macs_gsize                 = 2700000000
     macs2_narrow_peak          = true
     macs2_broad_cutoff         = 0.1
 
     // Consensus Peaks
     consensus_peak_mode        = 'group'
-    replicate_threshold        = 1.0
+    replicate_threshold        = 1
 
     // Reporting and Visualisation
     skip_reporting             = false
@@ -289,7 +289,14 @@ 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
+}
+
+validation {
+    help {
+        enabled = true
+        command = "nextflow run my_pipeline --input input_file.csv"
+    }
 }
 
 // Load igenomes.config if required

nextflow_schema.json

@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/cutandrun/master/nextflow_schema.json",
     "title": "nf-core/cutandrun pipeline parameters",
     "description": "Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes sequencing QC, spike-in normalisation, IgG control normalisation, peak calling and downstream peak analysis.",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -393,7 +393,7 @@
                     "description": "P-value threshold for macs2 peak caller. If set it will overide the qvalue."
                 },
                 "macs_gsize": {
-                    "type": "number",
+                    "type": "integer",
                     "default": 2700000000,
                     "fa_icon": "fas fa-align-justify",
                     "description": "parameter required by MACS2. If using an iGenomes reference these have been provided when `--genome` is set as *GRCh37*, *GRCh38*, *GRCm38*, *WBcel235*, *BDGP6*, *R64-1-1*, *EF2*, *hg38*, *hg19* and *mm10*. Otherwise the gsize will default to GRCh38."
@@ -418,7 +418,7 @@
                     "enum": ["group", "all"]
                 },
                 "replicate_threshold": {
-                    "type": "number",
+                    "type": "integer",
                     "default": 1,
                     "fa_icon": "fas fa-align-justify",
                     "description": "Minimum number of overlapping replicates needed for a consensus peak"
@@ -705,31 +705,31 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/reference_data_options"
+            "$ref": "#/$defs/reference_data_options"
         },
         {
-            "$ref": "#/definitions/flow_switching_options"
+            "$ref": "#/$defs/flow_switching_options"
         },
         {
-            "$ref": "#/definitions/trimming_options"
+            "$ref": "#/$defs/trimming_options"
         },
         {
-            "$ref": "#/definitions/pipeline_options"
+            "$ref": "#/$defs/pipeline_options"
         },
         {
-            "$ref": "#/definitions/reporting_options"
+            "$ref": "#/$defs/reporting_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"
         }
     ]
 }

workflows/cutandrun.nf

@@ -4,7 +4,7 @@
 ========================================================================================
 */
 
-include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
+include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-schema'
 
 // Validate input parameters in specialised library
 WorkflowCutandrun.initialise(params, log)