monochrome logs and prek all files fix

Author: vagkaratzas

.nf-core.yml

@@ -21,4 +21,4 @@ template:
   skip_features:
     - fastqc
     - igenomes
-  version: 1.1.0dev
+  version: 1.1.0dev

subworkflows/local/utils_nfcore_proteinannotator_pipeline/main.nf

@@ -27,7 +27,7 @@ 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
+    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
     input             //  string: Path to input samplesheet