pre-commit

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changes
 
 1. Added the `--squash-ploidy` argument to the RTG vcfeval process.
+2. Update to nf-core v3.0.1
 
 ### Fixes
 

main.nf

@@ -208,7 +208,7 @@ workflow {
         params.genome,
         params.watchdir
     )
-    
+
     //
     // WORKFLOW: Run main workflow
     //

nextflow.config

@@ -314,14 +314,14 @@ validation {
         showHiddenParameter = "show_hidden"
         beforeText = """
 -\033[2m----------------------------------------------------\033[0m-
-                                       \033[0;34m    ///\033[0;32m/// \033[0m
-\033[0;34m        ___     __   _  _   __   __    \033[0;34m  ///\033[0;32m///// \033[0m
-\033[0;34m  |\\ | |__  __ /  ` | \\/ | / _` / _`   \033[0;34m////\033[0;32m////// \033[0m
-\033[0;34m  | \\| |       \\__, |    | \\__| \\__|   \033[0;34m///\033[0;32m///// \033[0m
-                                       \033[0;34m///\033[0;32m/// \033[0m
+                                        \033[0;34m    ///\033[0;32m/// \033[0m
+\033[0;34m        ___     __   _  _   __   __     \033[0;34m  ///\033[0;32m///// \033[0m
+\033[0;34m  |\\ | |__  __ /  ` | \\/ | / _` / _`    \033[0;34m////\033[0;32m////// \033[0m
+\033[0;34m  | \\| |       \\__, |    | \\__| \\__|    \033[0;34m///\033[0;32m///// \033[0m
+                                        \033[0;34m///\033[0;32m/// \033[0m
 \033[0;35m  ${manifest.name} ${manifest.version}\033[0m
 -\033[2m----------------------------------------------------\033[0m-
-"""      
+"""
     }
 }
 

subworkflows/local/utils_cmgg_germline_pipeline/main.nf

@@ -51,7 +51,7 @@ workflow PIPELINE_INITIALISATION {
         workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
     )
 
-    
+
     //
     // Validate parameters and generate parameter summary to stdout
     //
@@ -60,7 +60,7 @@ workflow PIPELINE_INITIALISATION {
         validate_params,
         null
     )
-    
+
 
     //
     // Check config provided to the pipeline
@@ -104,7 +104,7 @@ workflow PIPELINE_COMPLETION {
     email           //  string: email address
     email_on_fail   //  string: email address sent on pipeline failure
     plaintext_email // boolean: Send plain-text email instead of HTML
-    
+
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
     hook_url        //  string: hook URL for notifications
@@ -192,7 +192,6 @@ def toolCitationText() {
 
 def toolBibliographyText() {
     def reference_text = [
-
             "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
         ].join(' ').trim()