Apply some linting

nf-core · May 10, 2024 · cae2c9e · cae2c9e
1 parent bc4ab38
commit cae2c9e
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Showing 4 changed files with 10 additions and 9 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -1,4 +1,4 @@
-    /*
+/*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Config file for defining DSL2 per module options and publishing paths
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
@@ -152,6 +152,7 @@ class WorkflowMain {
                     params.ref_data_panel_data_path = Constants.TSO500_PANEL_38_PATH
                 }
             }
+
         }
 
         def stages = Processes.getRunStages(
@@ -296,7 +297,9 @@ class WorkflowMain {
                     System.exit(1)
                 }
             }
+
         }
+
     }
 
     public static getRunConfig(params, inputs, log) {

diff --git a/modules/local/markdups/main.nf b/modules/local/markdups/main.nf
@@ -25,17 +25,15 @@ process MARKDUPS {
     task.ext.when == null || task.ext.when
 
     script:
-    // previously: def umi_flags = has_umis ? '-umi_enabled -umi_duplex -umi_duplex_delim +' : ''
-
     def umi_flags
-      if(has_umis) {
+    if(has_umis) {
         umi_flags = '-umi_enabled'
         if(umi_duplex_delim) {
-          umi_flags = "${umi_flags} -umi_duplex -umi_duplex_delim ${umi_duplex_delim}"
+            umi_flags = "${umi_flags} -umi_duplex -umi_duplex_delim ${umi_duplex_delim}"
         }
-      } else {
+    } else {
         umi_flags = '-form_consensus'
-      }
+    }
 
     """
     markdups \\

diff --git a/workflows/wgts.nf b/workflows/wgts.nf
@@ -146,7 +146,7 @@ workflow WGTS {
             ref_data.genome_bwa_index_bseq,
             ref_data.genome_bwa_index_biidx,
             params.max_fastq_records,
-            0, // disabled for now
+            0,  // disabled for now
         )
 
         READ_ALIGNMENT_RNA(
@@ -189,7 +189,7 @@ workflow WGTS {
             ref_data.genome_dict,
             hmf_data.unmap_regions,
             false,  // has_umis
-            "", // no duplex UMI delimiter
+            '',  // no duplex UMI delimiter
         )
 
         ch_versions = ch_versions.mix(READ_PROCESSING.out.versions)