update branch

CHANGELOG.md

@@ -7,6 +7,8 @@
 - Turn on automatic clean up of intermediate files in `work/` on successful pipeline completion in full-test config ([#2163](https://github.com/nf-core/tools/pull/2163)) [Contributed by @jfy133]
 - Add documentation to `usage.md` on how to use `params.yml` files, based on nf-core/ampliseq text ([#2173](https://github.com/nf-core/tools/pull/2173/)) [Contributed by @jfy133, @d4straub]
 - Make jobs automatically resubmit for a much wider range of exit codes (now `104` and `130..145`) ([#2170](https://github.com/nf-core/tools/pull/2170))
+- Remove shcema validation from `lib` folder and use Nextflow nf-validation plugin instead ([#1771](https://github.com/nf-core/tools/pull/1771/))
+- Generate input channel from input file using Nextflow nf-validation plugin ([#1771](https://github.com/nf-core/tools/pull/1771/))
 
 ### Linting
 

nf_core/pipeline-template/assets/schema_input.json

@@ -10,7 +10,8 @@
             "sample": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces"
+                "errorMessage": "Sample name must be provided and cannot contain spaces",
+                "meta": ["id"]
             },
             "fastq_1": {
                 "type": "string",

nf_core/pipeline-template/lib/WorkflowMain.groovy

@@ -18,60 +18,17 @@ class WorkflowMain {
             "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
     }
 
-    //
-    // Generate help string
-    //
-    public static String help(workflow, params, log) {
-        {% if igenomes -%}
-        def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
-        {% else -%}
-        def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --fasta reference.fa -profile docker"
-        {% endif -%}
-        def help_string = ''
-        help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs)
-        help_string += NfcoreSchema.paramsHelp(workflow, params, command)
-        help_string += '\n' + citation(workflow) + '\n'
-        help_string += NfcoreTemplate.dashedLine(params.monochrome_logs)
-        return help_string
-    }
-
-    //
-    // Generate parameter summary log string
-    //
-    public static String paramsSummaryLog(workflow, params, log) {
-        def summary_log = ''
-        summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs)
-        summary_log += NfcoreSchema.paramsSummaryLog(workflow, params)
-        summary_log += '\n' + citation(workflow) + '\n'
-        summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs)
-        return summary_log
-    }
-
     //
     // Validate parameters and print summary to screen
     //
     public static void initialise(workflow, params, log) {
-        // Print help to screen if required
-        if (params.help) {
-            log.info help(workflow, params, log)
-            System.exit(0)
-        }
-
         // Print workflow version and exit on --version
         if (params.version) {
             String workflow_version = NfcoreTemplate.version(workflow)
             log.info "${workflow.manifest.name} ${workflow_version}"
             System.exit(0)
         }
 
-        // Print parameter summary log to screen
-        log.info paramsSummaryLog(workflow, params, log)
-
-        // Validate workflow parameters via the JSON schema
-        if (params.validate_params) {
-            NfcoreSchema.validateParameters(workflow, params, log)
-        }
-
         // Check that a -profile or Nextflow config has been provided to run the pipeline
         NfcoreTemplate.checkConfigProvided(workflow, log)
 

nf_core/pipeline-template/nextflow.config

@@ -58,6 +58,10 @@ params {
     max_cpus                   = 16
     max_time                   = '240.h'
 
+    // Schema validation default options
+    fail_unrecognised_params   = false
+    lenient_mode               = false
+
 }
 
 // Load base.config by default for all pipelines

nf_core/pipeline-template/workflows/pipeline.nf

@@ -4,19 +4,36 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
+include { validateParameters            } from 'plugin/nf-validation'
+include { paramsHelp                    } from 'plugin/nf-validation'
+include { paramsSummaryLog              } from 'plugin/nf-validation'
+include { paramsSummaryMap              } from 'plugin/nf-validation'
+include { validateAndConvertSamplesheet } from 'plugin/nf-validation'
+
+def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
+def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
+def summary_params = paramsSummaryMap(workflow)
+
+// Print help message if needed
+if (params.help) {
+    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
+validateParameters()
+
+// Print parameter summary log to screen
+log.info logo + paramsSummaryLog(workflow) + citation
+
 Workflow{{ short_name[0]|upper }}{{ short_name[1:] }}.initialise(params, log)
 
 // TODO nf-core: Add all file path parameters for the pipeline to the list below
 // Check input path parameters to see if they exist
 def checkPathParamList = [ params.input, params.multiqc_config, params.fasta ]
 for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
 
-// Check mandatory parameters
-if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     CONFIG FILES
@@ -37,7 +54,6 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil
 //
 // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
 //
-include { INPUT_CHECK } from '../subworkflows/local/input_check'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -66,18 +82,18 @@ workflow {{ short_name|upper }} {
     ch_versions = Channel.empty()
 
     //
-    // SUBWORKFLOW: Read in samplesheet, validate and stage input files
+    // Create input channel from input file
     //
-    INPUT_CHECK (
-        ch_input
+    ch_input = Channel.validateAndConvertSamplesheet(
+        file(params.input, checkIfExists:true),
+        file("${projectDir}/assets/schema_input.json", checkIfExists:true)
     )
-    ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
 
     //
     // MODULE: Run FastQC
     //
     FASTQC (
-        INPUT_CHECK.out.reads
+        ch_input
     )
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())