From b742bffccf8c233de92a157d513cf373e06382c9 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 21 Feb 2019 11:56:37 +0100
Subject: [PATCH] explain the why
---
biopet/biopet.wdl | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/biopet/biopet.wdl b/biopet/biopet.wdl
index 3c7ac7b..86ca380 100644
--- a/biopet/biopet.wdl
+++ b/biopet/biopet.wdl
@@ -248,9 +248,13 @@ task ScatterRegions {
Int memory = 4
Float memoryMultiplier = 3.0
String dockerTag = "0.2--0"
- String outputDirPath = "scatters"
}
+ # OutDirPath must be defined here because the glob process relies on
+ # linking. This path must be in the containers filesystem, otherwise the
+ # linking does not work.
+ String outputDirPath = "scatters"
+
command {
set -e -o pipefail
mkdir -p ~{outputDirPath}
--
GitLab