mount points changed with GCP batch: mnt/disks/cromwell_root

stellaning1120 · stellaning1120 · commit aa95652b35d0 · 2025-07-23T19:00:04.000-04:00
diff --git a/wdl/tasks/VariantCalling/CCSPepper.wdl b/wdl/tasks/VariantCalling/CCSPepper.wdl
@@ -175,7 +175,7 @@ task DV {
     }
 
     String prefix = basename(bam, ".bam") + ".deepvariant"
-    String output_root = "/cromwell_root/dv_output"
+    String output_root = "/mnt/disks/cromwell_root/dv_output"
 
     Int bam_sz = ceil(size(bam, "GB"))
     Boolean is_big_bam = bam_sz > 100

Original file line number	Diff line number	Diff line change
`@@ -175,7 +175,7 @@ task DV {`
`175`	`175`	`}`
`176`	`176`
`177`	`177`	`String prefix = basename(bam, ".bam") + ".deepvariant"`
`178`		`- String output_root = "/cromwell_root/dv_output"`
	`178`	`+ String output_root = "/mnt/disks/cromwell_root/dv_output"`
`179`	`179`
`180`	`180`	`Int bam_sz = ceil(size(bam, "GB"))`
`181`	`181`	`Boolean is_big_bam = bam_sz > 100`