From ff2945526585a8ea9d937ce2a7bdea09a000fef0 Mon Sep 17 00:00:00 2001
From: Martin Proks <martin.proks@sund.ku.dk>
Date: Fri, 2 Aug 2024 10:39:51 +0200
Subject: [PATCH] fix: more coding style fixes

---
 conf/genomes.config                     |  2 +-
 subworkflows/local/make_count_matrix.nf |  2 +-
 subworkflows/local/starsolo.nf          |  2 +-
 workflows/primeseq.nf                   | 12 ++++++------
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/conf/genomes.config b/conf/genomes.config
index af02b70..ea51193 100644
--- a/conf/genomes.config
+++ b/conf/genomes.config
@@ -11,4 +11,4 @@ params {
             star        = "${params.genomes_base}/homo_sapiens/10x/refdata-gex-GRCh38-2024-A/star_2.7.10b"
         }
     }
-}
\ No newline at end of file
+}
diff --git a/subworkflows/local/make_count_matrix.nf b/subworkflows/local/make_count_matrix.nf
index e8d12bf..0e3fa63 100644
--- a/subworkflows/local/make_count_matrix.nf
+++ b/subworkflows/local/make_count_matrix.nf
@@ -10,7 +10,7 @@ workflow MAKE_COUNT_MATRIX {
     ch_versions = Channel.empty()
 
     MTX_TO_CSV ( reads )
-    
+
     ch_versions = ch_versions.mix(MTX_TO_CSV.out.versions.first())
 
     emit:
diff --git a/subworkflows/local/starsolo.nf b/subworkflows/local/starsolo.nf
index b3f3c94..642252d 100644
--- a/subworkflows/local/starsolo.nf
+++ b/subworkflows/local/starsolo.nf
@@ -11,7 +11,7 @@ workflow STARSOLO {
     ch_versions = Channel.empty()
 
     STARSOLO_ALIGN ( reads, index )
-    
+
     ch_versions = ch_versions.mix(STARSOLO_ALIGN.out.versions.first())
 
     emit:
diff --git a/workflows/primeseq.nf b/workflows/primeseq.nf
index 8d96aac..4575560 100644
--- a/workflows/primeseq.nf
+++ b/workflows/primeseq.nf
@@ -43,20 +43,20 @@ workflow PRIMESEQ {
     //
     // MODULE: Run STARSolo
     //
-    ch_reads = ch_samplesheet.map { 
-        meta, fastq -> [ 
-            [ 
-                id: meta.id, 
+    ch_reads = ch_samplesheet.map {
+        meta, fastq -> [
+            [
+                id: meta.id,
                 plate_id: meta.plate_id,
                 whitelist: ,
                 umi_len: 16,
                 umi_start: 13,
                 cb_len: 12,
                 cb_start: 1,
-            ], "CB_UMI_Simple", fastq 
+            ], "CB_UMI_Simple", fastq
         ]
     }
-    STARSOLO ( 
+    STARSOLO (
         ch_reads,
         file("$projectDir/assets/whitelist.tsv", checkIfExists: true),
         ch_star_index