From 7dc642847fd4851ca9a75b6808ecd1318dd1781f Mon Sep 17 00:00:00 2001
From: cagaser <c.agaser@lumc.nl>
Date: Fri, 21 Jun 2019 11:24:13 +0200
Subject: [PATCH] add SV task: delly.wdl
---
delly.wdl | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
create mode 100644 delly.wdl
diff --git a/delly.wdl b/delly.wdl
new file mode 100644
index 0000000..2fc63cd
--- /dev/null
+++ b/delly.wdl
@@ -0,0 +1,30 @@
+version 1.0
+
+import "common.wdl"
+
+task CallSV {
+ input {
+ IndexedBamFile bamFile
+ Reference reference
+ String outputPath
+ }
+
+
+ command <<<
+ set -e
+ mkdir -p $(dirname ~{outputPath})
+ delly call \
+ -o ~{outputPath} \
+ -g ~{reference.fasta} \
+ ~{bamFile.file}
+ >>>
+
+ output {
+ File dellyBcf = "~{outputPath}"
+ }
+
+ runtime {
+ docker: "quay.io/biocontainers/delly:0.8.1--h4037b6b_1"
+ }
+
+}
--
GitLab