Removed validate_params

Plant-Food-Research-Open · Oct 9, 2024 · 67db39d · 67db39d
1 parent 7afc159
commit 67db39d
Show file tree

Hide file tree

Showing 7 changed files with 15 additions and 28 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -22,7 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 1. Reduced the GenomeTools stats figures to 300 DPI [#142](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/142)
 2. Now `synteny_mummer_min_bundle_size` is set to `1000000` by default [#142](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/142)
 3. `results` is not the default output directory anymore
-4. Removed a number of unnecessary parameters: `monochromeLogs`, `config_profile_contact`, `config_profile_url`, `validationFailUnrecognisedParams`, `validationLenientMode`, `validationSchemaIgnoreParams`, `validationShowHiddenParams`
+4. Removed a number of unnecessary parameters: `monochromeLogs`, `config_profile_contact`, `config_profile_url`, `validationFailUnrecognisedParams`, `validationLenientMode`, `validationSchemaIgnoreParams`, `validationShowHiddenParams` `validate_params`
 5. Resource parameters have been removed: `max_memory`, `max_cpus`, `max_time`
 
 ## v2.1.1 - [20-Sep-2024]

diff --git a/conf/test.config b/conf/test.config
@@ -12,8 +12,8 @@
 
 process {
     resourceLimits = [
-        cpus: 2,
-        memory: '6.GB',
+        cpus: 4,
+        memory: '15.GB',
         time: '1.h'
     ]
 }

diff --git a/docs/parameters.md b/docs/parameters.md
@@ -124,13 +124,12 @@ Parameters used to describe centralised config profiles. These should not be edi
 
 Less common options for the pipeline, typically set in a config file.
 
-| Parameter                          | Description                                                             | Type      | Default | Required | Hidden |
-| ---------------------------------- | ----------------------------------------------------------------------- | --------- | ------- | -------- | ------ |
-| `help`                             | Display help text.                                                      | `boolean` |         |          | True   |
-| `version`                          | Display version and exit.                                               | `boolean` |         |          | True   |
-| `publish_dir_mode`                 | Method used to save pipeline results to output directory.               | `string`  | copy    |          | True   |
-| `email_on_fail`                    | Email address for completion summary, only when pipeline fails.         | `string`  |         |          | True   |
-| `plaintext_email`                  | Send plain-text email instead of HTML.                                  | `boolean` |         |          | True   |
-| `monochrome_logs`                  | Do not use coloured log outputs.                                        | `boolean` |         |          | True   |
-| `hook_url`                         | Incoming hook URL for messaging service                                 | `string`  |         |          | True   |
-| `validate_params`                  | Boolean whether to validate parameters against the schema at runtime    | `boolean` | True    |          | True   |
+| Parameter          | Description                                                     | Type      | Default | Required | Hidden |
+| ------------------ | --------------------------------------------------------------- | --------- | ------- | -------- | ------ |
+| `help`             | Display help text.                                              | `boolean` |         |          | True   |
+| `version`          | Display version and exit.                                       | `boolean` |         |          | True   |
+| `publish_dir_mode` | Method used to save pipeline results to output directory.       | `string`  | copy    |          | True   |
+| `email_on_fail`    | Email address for completion summary, only when pipeline fails. | `string`  |         |          | True   |
+| `plaintext_email`  | Send plain-text email instead of HTML.                          | `boolean` |         |          | True   |
+| `monochrome_logs`  | Do not use coloured log outputs.                                | `boolean` |         |          | True   |
+| `hook_url`         | Incoming hook URL for messaging service                         | `string`  |         |          | True   |
diff --git a/main.nf b/main.nf
@@ -66,7 +66,6 @@ workflow {
     //
     PIPELINE_INITIALISATION (
         params.version,
-        params.validate_params,
         params.monochrome_logs,
         args,
         params.outdir,

diff --git a/nextflow.config b/nextflow.config
@@ -90,10 +90,6 @@ params {
     config_profile_description          = null
     custom_config_version               = 'master'
     custom_config_base                  = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
-
-    // Schema validation default options
-    validate_params                     = true
-
 }
 
 // Max resources
@@ -292,6 +288,7 @@ validation {
         fullParameter = "help_full"
         showHiddenParameter = "show_hidden"
     }
+    monochromeLogs = params.monochrome_logs
 }
 
 // Load modules.config for DSL2 module specific options

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -428,13 +428,6 @@
                     "description": "Incoming hook URL for messaging service",
                     "fa_icon": "fas fa-people-group",
                     "hidden": true
-                },
-                "validate_params": {
-                    "type": "boolean",
-                    "description": "Boolean whether to validate parameters against the schema at runtime",
-                    "default": true,
-                    "fa_icon": "fas fa-check-square",
-                    "hidden": true
                 }
             }
         }

diff --git a/subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf b/subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf
@@ -29,7 +29,6 @@ workflow PIPELINE_INITIALISATION {
 
     take:
     version           // boolean: Display version and exit
-    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
     outdir            //  string: The output directory where the results will be saved
@@ -56,8 +55,8 @@ workflow PIPELINE_INITIALISATION {
     //
     UTILS_NFSCHEMA_PLUGIN (
         workflow,
-        validate_params,
-        null
+        true, // validate params
+        null // schema path: nextflow_schema
     )