feat(nf-schema): replace [email protected] by [email protected]

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 '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id '[email protected]' // 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",
     "$id": "https://raw.githubusercontent.com/nf-core/rnaseq/master/nextflow_schema.json",
     "title": "nf-core/rnaseq pipeline parameters",
     "description": "RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.",
     "type": "object",
-    "definitions": {
+    "defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -839,40 +839,40 @@
     },
     "allOf": [
         {
-            "$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) {