From e9189a7f5d61a46d1deec0108900a11d70630933 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hexylena@galaxians.org>
Date: Fri, 6 Jun 2025 10:55:53 +0200
Subject: [PATCH] missing trailing slash breaks samtools flagstat

---
 samtools.wdl | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/samtools.wdl b/samtools.wdl
index 743fce0c..ac2e868a 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -296,9 +296,10 @@ task Flagstat {
     command {
         set -e
         mkdir -p "$(dirname ~{outputPath})"
+
         samtools flagstat \
-        --threads ~{threads - 1}
-        ~{inputBam} > ~{outputPath}
+            --threads ~{threads - 1} \
+            ~{inputBam} > ~{outputPath}
     }
 
     output {