[Concatenate_Illumina_Lanes] Fix bug when single-end only (#695)

* quote it * remove duplicate set -euo pipefail
theiagen · Dec 17, 2024 · 2571a4f · 2571a4f
1 parent 4fbb73e
commit 2571a4f
Showing 1 changed file with 1 addition and 3 deletions.
diff --git a/tasks/utilities/file_handling/task_cat_lanes.wdl b/tasks/utilities/file_handling/task_cat_lanes.wdl
@@ -28,11 +28,9 @@ task cat_lanes {
 
     exists() { [[ -f $1 ]]; }
 
-    set -euo pipefail
-
     cat ~{read1_lane1} ~{read1_lane2} ~{read1_lane3} ~{read1_lane4} > "~{samplename}_merged_R1.fastq.gz"
 
-    if exists ~{read2_lane1} ; then
+    if exists "~{read2_lane1}" ; then
       cat ~{read2_lane1} ~{read2_lane2} ~{read2_lane3} ~{read2_lane4} > "~{samplename}_merged_R2.fastq.gz"
     fi