From 1a5287bd1875276df77bbd25b8c22e4f47ac727a Mon Sep 17 00:00:00 2001
From: golu099 <flavianegrete@gmail.com>
Date: Tue, 28 Nov 2023 16:01:05 -0500
Subject: [PATCH] outBam fixes

---
 pipes/WDL/tasks/tasks_megablast.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pipes/WDL/tasks/tasks_megablast.wdl b/pipes/WDL/tasks/tasks_megablast.wdl
index c0b62fc0a..6abcc0b4f 100755
--- a/pipes/WDL/tasks/tasks_megablast.wdl
+++ b/pipes/WDL/tasks/tasks_megablast.wdl
@@ -37,9 +37,9 @@ task trim_rmdup_subsamp {
     command <<<
         set -ex o pipefail
         assembly.py --version | tee VERSION
+        cat> "~{outBam}"
         #BAM ->FASTQ-> OutBam? https://github.com/broadinstitute/viral-assemble/blob/80bcc1da5c6a0174362ca9fd8bc0b49ee0b4103b/assembly.py#L91
         assembly.py trim_rmdup_subsamp_reads \
-        touch "~{outBam}"
         #if you suspect spaces in the filename use ""
         "~{inBam}" \
         "~{clipDb}" \