From 3565efa43b0ee9ec0aa030c5624986099232a4ee Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B3nio=20Paulo?= <antonio.do.paulo@ist.utl.pt>
Date: Sun, 4 Aug 2019 21:42:18 +0200
Subject: [PATCH] add modify_Strelka as task
---
somaticseq.wdl | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
diff --git a/somaticseq.wdl b/somaticseq.wdl
index d1163b4..4a8b860 100644
--- a/somaticseq.wdl
+++ b/somaticseq.wdl
@@ -267,3 +267,30 @@ task ParallelSingleTrain {
docker: dockerImage
}
}
+
+task ModifyStrelka {
+ input {
+ String installDir = "/opt/somaticseq/vcfModifier" #the location in the docker image
+
+ File strelkaVCF
+ String? outputVCFName = basename(strelkaVCF, ".gz")
+
+ Int threads = 1
+ String dockerImage = "lethalfang/somaticseq:3.1.0"
+ }
+
+ command {
+ ~{installDir}/modify_Strelka.py \
+ -infile ~{strelkaVCF} \
+ -outfile ~{outputVCFName}
+ }
+
+ output {
+ File outputVcf = outputVCFName
+ }
+
+ runtime {
+ cpu: threads
+ docker: dockerImage
+ }
+}
--
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