Use custom function to join args for modules

ricardoi · Apr 21, 2021 · 2a1c820 · 2a1c820
1 parent 3753488
commit 2a1c820
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Showing 3 changed files with 11 additions and 7 deletions.
diff --git a/lib/Utils.groovy b/lib/Utils.groovy
@@ -89,4 +89,7 @@ class Utils {
         )
     }
 
+    static String joinModuleArgs(args_list) {
+        return ' ' + args_list.join(' ')
+    }
 }
diff --git a/workflows/illumina.nf b/workflows/illumina.nf
@@ -54,7 +54,8 @@ ch_ivar_variants_header_mqc = file("$projectDir/assets/headers/ivar_variants_hea
 def modules = params.modules.clone()
 
 def multiqc_options   = modules['illumina_multiqc']
-multiqc_options.args += params.multiqc_title ? " --title \"$params.multiqc_title\"" : ''
+multiqc_options.args += params.multiqc_title ? Utils.joinModuleArgs(["--title \"$params.multiqc_title\""]) : ''
+
 if (!params.skip_assembly) {
     multiqc_options.publish_files.put('assembly_metrics_mqc.csv','assembly')
 }
@@ -93,7 +94,7 @@ if (!params.save_reference) {
 }
 
 def ivar_trim_options   = modules['illumina_ivar_trim']
-ivar_trim_options.args += params.ivar_trim_noprimer ? "" : " -e"
+ivar_trim_options.args += params.ivar_trim_noprimer ? '' : Utils.joinModuleArgs(['-e'])
 
 def ivar_trim_sort_bam_options = modules['illumina_ivar_trim_sort_bam']
 if (params.skip_markduplicates) {
@@ -102,7 +103,7 @@ if (params.skip_markduplicates) {
 }
 
 def spades_options   = modules['illumina_spades']
-spades_options.args += params.spades_mode ? " --${params.spades_mode}" : ""
+spades_options.args += params.spades_mode ? Utils.joinModuleArgs(["--${params.spades_mode}"]) : ''
 
 include { INPUT_CHECK        } from '../subworkflows/local/input_check'             addParams( options: [:] )
 include { PREPARE_GENOME     } from '../subworkflows/local/prepare_genome_illumina' addParams( genome_options: publish_genome_options, index_options: publish_index_options, db_options: publish_db_options, bowtie2_build_options: bowtie2_build_options, bedtools_getfasta_options: bedtools_getfasta_options, collapse_primers_options: collapse_primers_options, snpeff_build_options: snpeff_build_options, makeblastdb_options: makeblastdb_options, kraken2_build_options: kraken2_build_options )
@@ -137,7 +138,7 @@ def bowtie2_align_options = modules['illumina_bowtie2_align']
 if (params.save_unaligned) { bowtie2_align_options.publish_files.put('fastq.gz','unmapped') }
 
 def markduplicates_options   = modules['illumina_picard_markduplicates']
-markduplicates_options.args += params.filter_duplicates ? " REMOVE_DUPLICATES=true" : ""
+markduplicates_options.args += params.filter_duplicates ?  Utils.joinModuleArgs(['REMOVE_DUPLICATES=true']) : ''
 
 include { FASTQC_FASTP           } from '../subworkflows/nf-core/fastqc_fastp'           addParams( fastqc_raw_options: modules['illumina_fastqc_raw'], fastqc_trim_options: modules['illumina_fastqc_trim'], fastp_options: fastp_options )
 include { ALIGN_BOWTIE2          } from '../subworkflows/nf-core/align_bowtie2'          addParams( align_options: bowtie2_align_options, samtools_options: modules['illumina_bowtie2_sort_bam']                                           )

diff --git a/workflows/nanopore.nf b/workflows/nanopore.nf
@@ -49,11 +49,11 @@ if (params.artic_minion_caller == 'medaka') {
 def modules = params.modules.clone()
 
 def artic_minion_options   = modules['nanopore_artic_minion']
-artic_minion_options.args += params.artic_minion_caller  == 'medaka' ? " --medaka" : ""
-artic_minion_options.args += params.artic_minion_aligner == 'bwa'    ? " --bwa"    : " --minimap2"
+artic_minion_options.args += params.artic_minion_caller  == 'medaka' ? Utils.joinModuleArgs(['--medaka']) : ''
+artic_minion_options.args += params.artic_minion_aligner == 'bwa'    ? Utils.joinModuleArgs(['--bwa'])    : Utils.joinModuleArgs(['--minimap2'])
 
 def multiqc_options   = modules['nanopore_multiqc']
-multiqc_options.args += params.multiqc_title ? " --title \"$params.multiqc_title\"" : ''
+multiqc_options.args += params.multiqc_title ? Utils.joinModuleArgs(["--title \"$params.multiqc_title\""]) : ''
 
 include { ARTIC_GUPPYPLEX       } from '../modules/local/artic_guppyplex'       addParams( options: modules['nanopore_artic_guppyplex'] )
 include { ARTIC_MINION          } from '../modules/local/artic_minion'          addParams( options: artic_minion_options                )
-Original file line number
+Diff line change
@@ Expand Up / @@ -89,4 +89,7 @@ class Utils { @@
             )
         }
+        static String joinModuleArgs(args_list) {
+            return ' ' + args_list.join(' ')
+        }
     }