migrate to nf-schema

CHANGELOG.md

@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changes
 
 1. Updated the pipeline template to nf-core v2.13.1
+2. Migrate from nf-validation to nf-schema
 
 ## v1.1.0 - Naive Junior - [15 Sep 2023]
 

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",
  "$id": "https://raw.githubusercontent.com/nf-cmgg/wisecondorx/master/assets/schema_input.json",
  "title": "nf-cmgg/wisecondorx pipeline - params.input schema",
  "description": "Schema for the file provided with params.input",
@@ -10,16 +10,19 @@
  "cram": {
  "type": "string",
  "pattern": "^\\S+\\.(b|cr)am$",
- "format": "file-path"
+ "format": "file-path",
+ "exists": true
  },
  "crai": {
  "type": "string",
  "pattern": "^\\S+\\.(b|cr)ai$",
- "format": "file-path"
+ "format": "file-path",
+ "exists": true
  },
  "gender": {
  "type": "string",
- "pattern": "^(male|female)$",
+ "errorMessage": "The gender needs to be either 'male' or 'female'",
+ "enum": ["male", "female"],
  "meta": ["gender"]
  }
  },

main.nf

@@ -25,9 +25,9 @@ params.fai = getGenomeAttribute('fai')
  IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
-include { paramsSummaryLog } from 'plugin/nf-validation'
-include { paramsHelp } from 'plugin/nf-validation'
-include { validateParameters } from 'plugin/nf-validation'
+include { paramsSummaryLog } from 'plugin/nf-schema'
+include { paramsHelp } from 'plugin/nf-schema'
+include { validateParameters } from 'plugin/nf-schema'
 include { WISECONDORX } from './workflows/wisecondorx'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_wisecondorx_pipeline'
 include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_wisecondorx_pipeline'

nextflow.config

@@ -57,10 +57,6 @@ params {
  max_time = '240.h'
 
  // Schema validation default options
- validationFailUnrecognisedParams = false
- validationLenientMode = false
- validationSchemaIgnoreParams = 'genomes,igenomes_base,test_data'
- validationShowHiddenParams = false
  validate_params = true
 
 }
@@ -192,7 +188,14 @@ 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 = false
+ defaultIgnoreParams = ['genomes','igenomes_base','test_data']
+ 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",
  "$id": "https://raw.githubusercontent.com/nf-cmgg/wisecondorx/master/nextflow_schema.json",
  "title": "nf-cmgg/wisecondorx pipeline parameters",
  "description": "A nextflow pipeline for creating references for WisecondorX",
  "type": "object",
- "definitions": {
+ "defs": {
  "input_output_options": {
  "title": "Input/output options",
  "type": "object",
@@ -325,22 +325,22 @@
  },
  "allOf": [
  {
- "$ref": "#/definitions/input_output_options"
+ "$ref": "#/defs/input_output_options"
  },
  {
- "$ref": "#/definitions/other_options"
+ "$ref": "#/defs/other_options"
  },
  {
- "$ref": "#/definitions/reference_genome_options"
+ "$ref": "#/defs/reference_genome_options"
  },
  {
- "$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"
  }
  ]
 }

subworkflows/local/utils_nfcore_wisecondorx_pipeline/main.nf

@@ -9,8 +9,8 @@
 */
 
 include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
-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 { 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'
@@ -81,7 +81,7 @@ workflow PIPELINE_INITIALISATION {
  // Create channel from input file provided through params.input
  //
 
- Channel.fromSamplesheet("input")
+ Channel.fromList(samplesheetToList(params.input, "assets/schema_input.json"))
  .set { ch_samplesheet }
 
  emit: