fix batch dir

broadinstitute · May 14, 2024 · 9704a24 · 9704a24
1 parent a2ebd1b
commit 9704a24
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/pipelines/skylab/snm3C/snm3C.wdl b/pipelines/skylab/snm3C/snm3C.wdl
@@ -314,7 +314,8 @@ task Hisat_paired_end {
         if [ ~{cromwell_root_dir} = "gcp" ]; then
             batch_dir="batch*/"
         else
-            batch_dir="~{cromwell_root_dir}/*/*/*/*/*/*/*/*/*/*/*/batch*/"
+            batch_dir="~{cromwell_root_dir}/*/*/*/*/*~{cromwell_root_dir}/*/*/*/*/batch*/"
+
         fi
 
         task() {