Added monochromeLogs parameter to suppress warnings

Plant-Food-Research-Open · Oct 8, 2024 · 21e90d1 · 21e90d1
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 
 1. Now using `${meta.id}_trim` as prefix for `FASTQC` files
+2. Added `monochromeLogs` parameter to suppress warnings
 
 ### `Dependencies`
 

diff --git a/docs/parameters.md b/docs/parameters.md
@@ -116,6 +116,7 @@ Less common options for the pipeline, typically set in a config file.
 | `plaintext_email`                  | Send plain-text email instead of HTML.                                  | `boolean` |                                                          |          | True   |
 | `max_multiqc_email_size`           | File size limit when attaching MultiQC reports to summary emails.       | `string`  | 25.MB                                                    |          | True   |
 | `monochrome_logs`                  | Do not use coloured log outputs.                                        | `boolean` |                                                          |          | True   |
+| `monochromeLogs`                   | 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   |
 | `validationShowHiddenParams`       | Show all params when using `--help`                                     | `boolean` |                                                          |          | True   |

diff --git a/nextflow.config b/nextflow.config
@@ -72,6 +72,7 @@ params {
     email_on_fail                       = null
     plaintext_email                     = false
     monochrome_logs                     = false
+    monochromeLogs                      = false
     hook_url                            = null
     help                                = false
     version                             = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -444,6 +444,12 @@
                     "fa_icon": "fas fa-palette",
                     "hidden": true
                 },
+                "monochromeLogs": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-palette",
+                    "description": "Do not use coloured log outputs.",
+                    "hidden": true
+                },
                 "hook_url": {
                     "type": "string",
                     "description": "Incoming hook URL for messaging service",