Fix linting

conf/co2footprint.config

@@ -6,4 +6,5 @@ co2footprint {
     file        = "${params.outdir}/co2footprint.txt"
     reportFile  = "${params.outdir}/co2footprint_report.html"
     location    = "GB"
-}
+}
+

conf/modules.config

@@ -18,7 +18,6 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

conf/test.config

@@ -27,5 +27,4 @@ params {
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
 
-
 }

main.nf

@@ -74,7 +74,6 @@ workflow {
     PIPELINE_COMPLETION (
         params.outdir,
         params.monochrome_logs,
-
         SANGERTOL_LONGREADMAG.out.multiqc_report
     )
 }

nextflow.config

@@ -13,8 +13,6 @@ params {
     // Input options
     input                      = null
 
-
-
     // MultiQC options
     multiqc_config             = null
     multiqc_title              = null
@@ -26,7 +24,7 @@ params {
     outdir                       = null
     publish_dir_mode             = 'copy'
     monochrome_logs              = false
-    
+
     help                         = false
     help_full                    = false
     show_hidden                  = false
@@ -235,7 +233,6 @@ validation {
         command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
         fullParameter = "help_full"
         showHiddenParameter = "show_hidden"
-
     }
 }
 

subworkflows/local/utils_nfcore_longreadmag_pipeline/main.nf

@@ -101,7 +101,7 @@ workflow PIPELINE_COMPLETION {
     take:
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
-    
+
     multiqc_report  //  string: Path to MultiQC report
 
     main:
@@ -149,7 +149,6 @@ def toolCitationText() {
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def citation_text = [
             "Tools used in the workflow included:",
-
             "MultiQC (Ewels et al. 2016)",
             "."
         ].join(' ').trim()
@@ -162,7 +161,6 @@ def toolBibliographyText() {
     // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     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()