outBam fixes

broadinstitute · Nov 28, 2023 · 1a5287b · 1a5287b
1 parent f5ec74d
commit 1a5287b
Showing 1 changed file with 1 addition and 1 deletion.
diff --git 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}" \