Fix code style problems

nf-core · May 27, 2024 · f351b96 · f351b96
1 parent e6e3157
commit f351b96
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Showing 9 changed files with 24 additions and 24 deletions.
diff --git a/subworkflows/local/discovery/annotation.nf b/subworkflows/local/discovery/annotation.nf
@@ -9,7 +9,7 @@ workflow ANNOTATION {
     regions
     gtf
     exon_boundary
-    
+
     main:
     ch_versions = Channel.empty()
 
@@ -35,4 +35,4 @@ workflow ANNOTATION {
     gtf = COMBINE_GTFS.out.sorted
 
     versions = ch_versions
-}
+}
diff --git a/subworkflows/local/discovery/circexplorer2.nf b/subworkflows/local/discovery/circexplorer2.nf
@@ -8,10 +8,10 @@ workflow CIRCEXPLORER2 {
     gtf
     fasta
     star_junctions
-    
+
     main:
     ch_versions = Channel.empty()
-    
+
     REFERENCE( gtf )
     PARSE( star_junctions )
     ANNOTATE( PARSE.out.junction, fasta, REFERENCE.out.txt )
@@ -27,4 +27,4 @@ workflow CIRCEXPLORER2 {
     bed   = UNIFY.out.output
 
     versions = ch_versions
-}
+}
diff --git a/subworkflows/local/discovery/circrna_finder.nf b/subworkflows/local/discovery/circrna_finder.nf
@@ -7,22 +7,22 @@ workflow CIRCRNA_FINDER {
     star_sam
     star_junctions
     star_tab
-    
+
     main:
     ch_versions = Channel.empty()
 
     ch_joined = star_sam.join(star_junctions).join(star_tab)
-        .map{ meta, sam, junction, tab -> 
+        .map{ meta, sam, junction, tab ->
             [ meta + [tool: "circrna_finder"], [sam, junction, tab] ] }
-    
+
     MAIN( ch_joined )
     UNIFY( MAIN.out.results, [] )
 
     ch_versions = ch_versions.mix(MAIN.out.versions)
     ch_versions = ch_versions.mix(UNIFY.out.versions)
-    
+
     emit:
     bed = UNIFY.out.output
 
     versions = ch_versions
-}
+}
diff --git a/subworkflows/local/discovery/ciriquant.nf b/subworkflows/local/discovery/ciriquant.nf
@@ -8,7 +8,7 @@ workflow CIRIQUANT {
     ch_fasta
     bwa_index
     hisat2_index
-    
+
     main:
     ch_versions = Channel.empty()
 
@@ -23,4 +23,4 @@ workflow CIRIQUANT {
     bed = UNIFY.out.output
 
     versions = ch_versions
-}
+}
diff --git a/subworkflows/local/discovery/dcc.nf b/subworkflows/local/discovery/dcc.nf
@@ -18,10 +18,10 @@ workflow DCC {
     seq_platform
     seq_center
     bsj_reads
-    
+
     main:
     ch_versions = Channel.empty()
-    
+
     mate1 = reads.filter{ meta, reads -> !meta.single_end }
         .map{ meta, reads -> return [ [id: meta.id, single_end: true], reads[0] ] }
     MATE1_1ST_PASS( mate1, star_index, ch_gtf, ignore_sjdbgtf, seq_platform, seq_center )
@@ -62,6 +62,6 @@ workflow DCC {
 
     emit:
     bed = UNIFY.out.output
-    
+
     versions = ch_versions
-}
+}
diff --git a/subworkflows/local/discovery/find_circ.nf b/subworkflows/local/discovery/find_circ.nf
@@ -10,7 +10,7 @@ workflow FIND_CIRC {
     reads
     bowtie2_index
     ch_fasta
-    
+
     main:
     ch_versions = Channel.empty()
 
@@ -33,4 +33,4 @@ workflow FIND_CIRC {
     bed = UNIFY.out.output
 
     versions = ch_versions
-}
+}
diff --git a/subworkflows/local/discovery/mapsplice.nf b/subworkflows/local/discovery/mapsplice.nf
@@ -12,7 +12,7 @@ workflow MAPSPLICE {
     bowtie_index
     chromosomes
     star_junctions
-    
+
     main:
     ch_versions = Channel.empty()
 
@@ -28,9 +28,9 @@ workflow MAPSPLICE {
     ch_versions = ch_versions.mix(PARSE.out.versions)
     ch_versions = ch_versions.mix(ANNOTATE.out.versions)
     ch_versions = ch_versions.mix(UNIFY.out.versions)
-    
+
     emit:
     bed = UNIFY.out.output
 
     versions = ch_versions
-}
+}
diff --git a/subworkflows/local/discovery/segemehl.nf b/subworkflows/local/discovery/segemehl.nf
@@ -24,4 +24,4 @@ workflow SEGEMEHL {
     bed = UNIFY.out.output
 
     versions = ch_versions
-}
+}
diff --git a/subworkflows/local/discovery/star2pass.nf b/subworkflows/local/discovery/star2pass.nf
@@ -12,7 +12,7 @@ workflow STAR2PASS {
     ignore_sjdbgtf
     seq_center
     seq_platform
-    
+
     main:
     ch_versions = Channel.empty()
 
@@ -31,4 +31,4 @@ workflow STAR2PASS {
     tab = PASS_2.out.tab
 
     versions = ch_versions
-}
+}