From 7590325b1a9b65b3362b45a03173062aed46342a Mon Sep 17 00:00:00 2001
From: Jannik Seidel <seidel.work@mailbox.org>
Date: Fri, 1 Nov 2024 12:30:33 +0100
Subject: [PATCH] removed trailing whitespaces

---
 workflows/detaxizer.nf | 66 +++++++++++++++++++++---------------------
 1 file changed, 33 insertions(+), 33 deletions(-)

diff --git a/workflows/detaxizer.nf b/workflows/detaxizer.nf
index 8cb972a..af77419 100644
--- a/workflows/detaxizer.nf
+++ b/workflows/detaxizer.nf
@@ -377,20 +377,20 @@ workflow NFCORE_DETAXIZER {
                 ( !params.validation_blastn && params.enable_filter ) || params.filter_with_classification
             ) && !params.filter_trimmed
         ) {
-        
+
         ch_classification = RENAME_FASTQ_HEADERS_PRE.out.fastq
             .join(MERGE_IDS.out.classified_ids, by:[0])
-        
+
         FILTER(
             ch_classification
         )
-        
+
         ch_versions = ch_versions.mix(FILTER.out.versions.first())
 
     } else if (
         params.enable_filter && !params.filter_trimmed
         ) {
-        
+
         ch_blastn2filter = FILTER_BLASTN_IDENTCOV.out.classified_ids.map {
             meta, path ->
                 return [ meta + [ id: meta.id.replaceAll("(_R1|_R2)", "") ], path ]
@@ -408,31 +408,31 @@ workflow NFCORE_DETAXIZER {
         ch_blastnfilter = ch_combined_short_long_id.join(
             ch_blastn2filter, by:[0]
         )
-        
+
         FILTER(
             ch_blastnfilter
         )
-        
+
         ch_versions = ch_versions.mix(FILTER.out.versions.first())
-    
+
     } else if (
         (
             ( !params.validation_blastn && params.enable_filter ) || params.filter_with_classification
         ) && params.filter_trimmed
     ){
-        
+
         ch_classification = ch_fastq_for_classification
             .join(MERGE_IDS.out.classified_ids, by:[0])
-        
+
         FILTER(
             ch_classification
         )
-        
+
         ch_versions = ch_versions.mix(FILTER.out.versions.first())
     } else if (
         params.enable_filter && params.filter_trimmed
     ){
-        
+
         ch_blastn2filter = FILTER_BLASTN_IDENTCOV.out.classified_ids.map {
             meta, path ->
                 return [ meta + [ id: meta.id.replaceAll("(_R1|_R2)", "") ], path ]
@@ -446,15 +446,15 @@ workflow NFCORE_DETAXIZER {
             meta, path ->
                 return [ meta + [ id: meta.id.replaceAll("(_R1|_R2)", "") ], path ]
         }
-        
+
         ch_blastnfilter = ch_combined_short_long_id.join(
             ch_blastn2filter, by:[0]
         )
-        
+
         FILTER(
             ch_blastnfilter
         )
-        
+
         ch_versions = ch_versions.mix(FILTER.out.versions.first())
     }
 
@@ -462,7 +462,7 @@ workflow NFCORE_DETAXIZER {
     // MODULE: Rename headers after filtering
     //
     if ( params.enable_filter ) {
-    
+
     ch_headers = RENAME_FASTQ_HEADERS_PRE.out.headers.map {
         meta, path ->
             return [ meta + [ id: meta.id.replaceAll("(_R1|_R2)", "") ], path ]
@@ -472,41 +472,41 @@ workflow NFCORE_DETAXIZER {
         meta, path ->
             return [ meta + [ id: meta.id.replaceAll("(_R1|_R2)", "") ], path ]
     }
-    
+
     ch_removed2rename = Channel.empty()
-    
+
     if ( params.output_removed_reads ){
         ch_removed2rename = FILTER.out.removed.map {
         meta, path ->
             return [ meta + [ id: meta.id.replaceAll("(_R1|_R2)", "") ], path ]
     }
     }
-    
+
     ch_rename_filtered = ch_filtered2rename.join(ch_headers, by:[0])
 
     ch_removed2rename = ch_removed2rename.ifEmpty(['empty', []])
-    
+
     if ( params.output_removed_reads ){
-    
+
         RENAME_FASTQ_HEADERS_AFTER(
         ch_rename_filtered,
         ch_removed2rename
         )
-    
+
         ch_versions = ch_versions.mix(RENAME_FASTQ_HEADERS_AFTER.out.versions.first())
-    
+
     } else {
-    
+
         RENAME_FASTQ_HEADERS_AFTER(
         ch_rename_filtered,
         ch_removed2rename.first()
-    
+
     )
-    
+
     ch_versions = ch_versions.mix(RENAME_FASTQ_HEADERS_AFTER.out.versions.first())
-    
+
     }
-    
+
     if ( params.classification_kraken2_post_filtering ) {
 
         KRAKEN2_POST_CLASSIFICATION_FILTERED (
@@ -515,18 +515,18 @@ workflow NFCORE_DETAXIZER {
             params.save_output_fastqs_filtered,
             true
             )
-    
+
         ch_versions = ch_versions.mix(KRAKEN2_POST_CLASSIFICATION_FILTERED.out.versions.first())
-    
+
         if (params.output_removed_reads) {
-    
+
             KRAKEN2_POST_CLASSIFICATION_REMOVED (
                 RENAME_FASTQ_HEADERS_AFTER.out.fastq_removed,
                 KRAKEN2PREPARATION.out.db.first(),
                 params.save_output_fastqs_removed,
                 true
                 )
-    
+
             ch_versions = ch_versions.mix(KRAKEN2_POST_CLASSIFICATION_REMOVED.out.versions.first())
 
         }
@@ -538,13 +538,13 @@ workflow NFCORE_DETAXIZER {
     // MODULE: Summarize the classification process
     //
     if (params.validation_blastn){
-    
+
     ch_summary = ch_classification_summary.mix(ch_blastn_summary).collect().map {
             item -> [['id': "summary_of_classification_and_blastn"], item]
         }
 
     } else {
-        
+
         ch_summary = ch_classification_summary.collect().map {
             item -> [['id': "summary_of_classification"], item]
         }