ththng · ththng · May 25, 2025 · May 25, 2025 · May 25, 2025
diff --git a/assets/schema_input.json b/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/minion/qcbench/master/assets/schema_input.json",
     "title": "minion-qcbench pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",

diff --git a/conf/base.config b/conf/base.config
@@ -11,9 +11,9 @@
 process {
 
     // TODO nf-core: Check the defaults for all processes
-    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
-    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
-    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
+    cpus   = { 1      * task.attempt }
+    memory = { 6.GB   * task.attempt }
+    time   = { 4.h    * task.attempt }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
     maxRetries    = 1
@@ -27,30 +27,30 @@ process {
     // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
-        cpus   = { check_max( 1                  , 'cpus'    ) }
-        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        cpus   = { 1                   }
+        memory = { 6.GB * task.attempt }
+        time   = { 4.h  * task.attempt }
     }
     withLabel:process_low {
-        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        cpus   = { 2     * task.attempt }
+        memory = { 12.GB * task.attempt }
+        time   = { 4.h   * task.attempt }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+        cpus   = { 6     * task.attempt }
+        memory = { 36.GB * task.attempt }
+        time   = { 8.h   * task.attempt }
     }
     withLabel:process_high {
-        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
-        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
+        cpus   = { 12    * task.attempt }
+        memory = { 72.GB * task.attempt }
+        time   = { 16.h  * task.attempt }
     }
     withLabel:process_long {
-        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+        time   = { 20.h  * task.attempt }
     }
     withLabel:process_high_memory {
-        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+        memory = { 200.GB * task.attempt }
     }
     withLabel:error_ignore {
         errorStrategy = 'ignore'

diff --git a/conf/test.config b/conf/test.config
@@ -10,19 +10,22 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
+
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     input  = params.pipelines_testdata_base_path + 'test_samplesheet.csv'
     outdir                     = 'results'
-    
+
     quality_scores             = '13,15'
     flye_modes                 = 'nano-raw,nano-corr'
 }
diff --git a/main.nf b/main.nf
@@ -59,14 +59,14 @@ workflow {
     //
     PIPELINE_INITIALISATION (
         params.version,
-        params.help,
+        // params.help,
         params.validate_params,
         params.monochrome_logs,
         args,
         params.outdir,
         params.input
     )
-    
+
     //
     // WORKFLOW: Run main workflow
     //

diff --git a/modules.json b/modules.json
@@ -43,6 +43,11 @@
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
+                    },
+                    "utils_nfschema_plugin": {
+                        "branch": "master",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }

diff --git a/nextflow.config b/nextflow.config
@@ -18,7 +18,7 @@ params {
 
     // Flye options
     flye_modes                 = null // fyle modes representing the underlying sequencing technology (supported options: pacbio-raw, pacbio-corr, pacbio-hifi, nano-raw, nano-corr, nano-hq)
-    flye_genome_size           = null // estimated genome size e.g. 4.4m 
+    flye_genome_size           = null // estimated genome size e.g. 4.4m
 
     // QUAST options
     quast_refseq               = null // path to reference genome file
@@ -38,19 +38,24 @@ params {
 
     // Max resource options
     // Defaults only, expecting to be overwritten
+    /*
     max_memory                 = '128.GB'
     max_cpus                   = 16
     max_time                   = '240.h'
+    */
 
-    // Schema validation default options
-    validationFailUnrecognisedParams = false
-    validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
-    validationShowHiddenParams       = false
     validate_params                  = true
 
 }
 
+process {
+    resourceLimits = [
+        cpus: 16,
+        memory: '128.GB',
+        time: '6.h'
+    ]
+}
+
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
@@ -166,7 +171,7 @@ 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@2.4.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
@@ -207,19 +212,27 @@ dag {
 manifest {
     name            = 'minion-qcbench'
     author          = """Thu Thao Nguyen"""
-    homePage        = 'https://github.com/minion/qcbench'
+    homePage        = 'https://github.com/ththng/minion-qcbench'
     description     = """Benchmarking quality control tools for MinION data"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=22.10.6'
+    nextflowVersion = '!>=24.0.0'
     version         = '1.0dev'
     doi             = ''
 }
 
+validation {
+    help {
+        enabled = true
+        command = "nextflow run ${manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR> --quality_scores <SCORE1,SCORE2,...> --flye_modes <FLYE_MODE1,FLYE_MODE2,...>"
+    }
+}
+
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'
 
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit
+/*
 def check_max(obj, type) {
     if (type == 'memory') {
         try {
@@ -250,3 +263,4 @@ def check_max(obj, type) {
         }
     }
 }
+*/
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/minion/qcbench/master/nextflow_schema.json",
     "title": "minion/qcbench pipeline parameters",
     "description": "Benchmarking quality control tools for MinION data",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -128,27 +128,6 @@
                     "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)."
-                },
                 "pipelines_testdata_base_path": {
                     "type": "string",
                     "fa_icon": "far fa-check-circle",
@@ -161,16 +140,16 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$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"
         }
     ],
     "properties": {

diff --git a/null/pipeline_info/execution_trace_2025-05-25_16-18-38.txt b/null/pipeline_info/execution_trace_2025-05-25_16-18-38.txt
@@ -0,0 +1 @@
+task_id	hash	native_id	name	status	exit	submit	duration	realtime	%cpu	peak_rss	peak_vmem	rchar	wchar
diff --git a/null/pipeline_info/execution_trace_2025-05-25_16-20-16.txt b/null/pipeline_info/execution_trace_2025-05-25_16-20-16.txt
@@ -0,0 +1 @@
+task_id	hash	native_id	name	status	exit	submit	duration	realtime	%cpu	peak_rss	peak_vmem	rchar	wchar
diff --git a/subworkflows/local/utils_nfcore_qcbench_pipeline/main.nf b/subworkflows/local/utils_nfcore_qcbench_pipeline/main.nf
@@ -9,8 +9,9 @@
 */
 
 include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
-include { paramsSummaryMap          } from 'plugin/nf-validation'
-include { fromSamplesheet           } from 'plugin/nf-validation'
+include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
+include { paramsSummaryMap          } from 'plugin/nf-schema'
+include { samplesheetToList         } from 'plugin/nf-schema'
 include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
 include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
@@ -27,7 +28,7 @@ workflow PIPELINE_INITIALISATION {
 
     take:
     version           // boolean: Display version and exit
-    help              // boolean: Display help text
+    // help              // boolean: Display help text
     validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
     monochrome_logs   // boolean: Do not use coloured log outputs
     nextflow_cli_args //   array: List of positional nextflow CLI args
@@ -51,17 +52,28 @@ workflow PIPELINE_INITIALISATION {
     //
     // Validate parameters and generate parameter summary to stdout
     //
+    /*
     pre_help_text = workflowHeader(monochrome_logs)
     post_help_text = '\n'
     def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR> --quality_scores <SCORE1,SCORE2,...> --flye_modes <FLYE_MODE1,FLYE_MODE2,...>"
     UTILS_NFVALIDATION_PLUGIN (
-        help,
-        workflow_command,
-        pre_help_text,
-        post_help_text,
+        // help,
+        // workflow_command,
+        // pre_help_text,
+        // post_help_text,
         validate_params,
         "nextflow_schema.json"
     )
+     */
+
+    //
+    // Validate parameters and generate parameter summary to stdout
+    //
+    UTILS_NFSCHEMA_PLUGIN (
+        workflow,
+        validate_params,
+        null
+    )
 
     //
     // Check config provided to the pipeline
@@ -74,7 +86,7 @@ workflow PIPELINE_INITIALISATION {
     // Create channel from input file provided through params.input
     //
     Channel
-        .fromSamplesheet("input")
+        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
         .map {
             meta, fastq ->
                 return [ meta + [ single_end:true ], [ fastq ] ]
@@ -141,7 +153,7 @@ def create_flye_samplesheet(ch_samplesheet, modes) {
             modes.collect { mode ->
                 [meta + [mode: mode], filePath]
             }
-        } 
+        }
         .multiMap { meta, fastq ->
             def mode_input = "--" + meta.mode
             samplesheet: [meta, fastq]

diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar