feat(nf-schema): replace nf-validation@1.3 by nf-schema@2.0.0

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/rnaseq/master/assets/schema_input.json",
     "title": "nf-core/rnaseq pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",

nextflow.config

@@ -127,11 +127,7 @@ params {
     max_time                   = '240.h'
 
     // Schema validation default options
-    validationFailUnrecognisedParams = false
-    validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
-    validationShowHiddenParams       = false
-    validate_params                  = true
+    validate_params            = true
 
 }
 
@@ -278,7 +274,14 @@ 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@2.0.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+}
+
+validation {
+    failUnrecognisedParams = false
+    lenientMode            = true
+    defaultIgnoreParams    = [ 'genomes', 'igenomes_base' ]
+    showHiddenParams       = false
 }
 
 // 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/rnaseq/master/nextflow_schema.json",
     "title": "nf-core/rnaseq pipeline parameters",
     "description": "RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.",
     "type": "object",
-    "definitions": {
+    "defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -812,67 +812,46 @@
                     "default": true,
                     "fa_icon": "fas fa-check-square",
                     "hidden": true
-                },
-                "validationShowHiddenParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-eye-slash",
-                    "description": "Show all params when using `--help`",
-                    "hidden": true,
-                    "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
-                },
-                "validationFailUnrecognisedParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters fails when an unrecognised parameter is found.",
-                    "hidden": true,
-                    "help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
-                },
-                "validationLenientMode": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters in lenient more.",
-                    "hidden": true,
-                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
                 }
             }
         }
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
+            "$ref": "#/defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/reference_genome_options"
+            "$ref": "#/defs/reference_genome_options"
         },
         {
-            "$ref": "#/definitions/read_trimming_options"
+            "$ref": "#/defs/read_trimming_options"
         },
         {
-            "$ref": "#/definitions/read_filtering_options"
+            "$ref": "#/defs/read_filtering_options"
         },
         {
-            "$ref": "#/definitions/umi_options"
+            "$ref": "#/defs/umi_options"
         },
         {
-            "$ref": "#/definitions/alignment_options"
+            "$ref": "#/defs/alignment_options"
         },
         {
-            "$ref": "#/definitions/optional_outputs"
+            "$ref": "#/defs/optional_outputs"
         },
         {
-            "$ref": "#/definitions/quality_control"
+            "$ref": "#/defs/quality_control"
         },
         {
-            "$ref": "#/definitions/process_skipping_options"
+            "$ref": "#/defs/process_skipping_options"
         },
         {
-            "$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/rnaseq/main.nf

@@ -52,8 +52,8 @@ include { BEDTOOLS_GENOMECOV as BEDTOOLS_GENOMECOV_REV         } from '../../mod
 //
 // SUBWORKFLOW: Consisting entirely of nf-core/modules
 //
-include { paramsSummaryMap                 } from 'plugin/nf-validation'
-include { fromSamplesheet                  } from 'plugin/nf-validation'
+include { paramsSummaryMap                 } from 'plugin/nf-schema'
+include { samplesheetToList                } from 'plugin/nf-schema'
 include { paramsSummaryMultiqc             } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML           } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
 include { FASTQ_SUBSAMPLE_FQ_SALMON        } from '../../subworkflows/nf-core/fastq_subsample_fq_salmon'
@@ -111,7 +111,7 @@ workflow RNASEQ {
     // Create channel from input file provided through params.input
     //
     Channel
-        .fromSamplesheet("input")
+        .fromList(samplesheetToList(params.input, "$projectDir/assets/schema_input.json"))
         .map {
             meta, fastq_1, fastq_2 ->
                 if (!fastq_2) {