From 842691aa0cf90ff2f88f4ea9c2c9122912111301 Mon Sep 17 00:00:00 2001 From: fraser-combe Date: Thu, 31 Oct 2024 15:27:33 -0500 Subject: [PATCH] clean tab/spaces echo --- .../basic_statistics/task_assembly_metrics.wdl | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tasks/quality_control/basic_statistics/task_assembly_metrics.wdl b/tasks/quality_control/basic_statistics/task_assembly_metrics.wdl index 8323dd3f1..359eb4ea1 100644 --- a/tasks/quality_control/basic_statistics/task_assembly_metrics.wdl +++ b/tasks/quality_control/basic_statistics/task_assembly_metrics.wdl @@ -53,14 +53,14 @@ task stats_n_coverage { #output all metrics in one txt file # Output header row (for CSV) - echo "Statistic Value" > ~{samplename}_metrics.txt + echo -e "Statistic\tValue" > ~{samplename}_metrics.txt # Output each statistic as a row - echo "Coverage $coverage" >> ~{samplename}_metrics.txt - echo "Depth $depth" >> ~{samplename}_metrics.txt - echo "Mean Base Quality $meanbaseq" >> ~{samplename}_metrics.txt - echo "Mean Mapping Quality $meanmapq" >> ~{samplename}_metrics.txt - echo "Percentage Mapped Reads $percentage_mapped_reads" >> ~{samplename}_metrics.txt + echo -e "Coverage\t$coverage" >> ~{samplename}_metrics.txt + echo -e "Depth\t$depth" >> ~{samplename}_metrics.txt + echo -e "Mean Base Quality\t$meanbaseq" >> ~{samplename}_metrics.txt + echo -e "Mean Mapping Quality\t$meanmapq" >> ~{samplename}_metrics.txt + echo -e "Percentage Mapped Reads\t$percentage_mapped_reads" >> ~{samplename}_metrics.txt >>> output { String date = read_string("DATE")