diff --git a/tasks/utilities/file_handling/task_cat_lanes.wdl b/tasks/utilities/file_handling/task_cat_lanes.wdl index 60a2b7d28..d3755eba9 100644 --- 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