From f9152ab2e1db5acff80244e83a7ed7e698f2c15f Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 27 Jul 2018 15:55:25 +0200
Subject: [PATCH] add Somatic strelka task
---
strelka.wdl | 47 +++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 47 insertions(+)
create mode 100644 strelka.wdl
diff --git a/strelka.wdl b/strelka.wdl
new file mode 100644
index 0000000..137efe9
--- /dev/null
+++ b/strelka.wdl
@@ -0,0 +1,47 @@
+version 1.0
+
+task Somatic {
+ input {
+ String? preCommand
+ String? installDir
+ String runDir
+ File normalBam
+ File tumorBam
+ File refFasta
+
+ Int cores = 1
+ Int memory = 4
+ }
+
+ String toolCommand = if defined(installDir)
+ then installDir + "bin/configureStrelkaSomaticWorkflow.py"
+ else "configureStrelkaSomaticWorkflow.py"
+
+ command {
+ set -e -o pipefail
+ ~{preCommand}
+ ~{toolCommand} \
+ --normalBam ~{normalBam} \
+ --tumorBam ~{tumorBam} \
+ --ref ~{refFasta} \
+ --runDir ~{runDir}
+
+ ~{runDir}/runWorkflow.py \
+ -m local \
+ -J ~{cores} \
+ -g ~{memory}
+ }
+
+ output {
+ String runDir = runDir
+ File indelsVcf = runDir + "/results/variants/somatic.indels.vcf.gz"
+ File indelsIndex = runDir + "/results/variants/somatic.indels.vcf.gz.tbi"
+ File snvVcf = runDir + "/results/variants/somatic.snvs.vcf.gz"
+ File snvIndex = runDir + "/results/variants/somatic.snvs.vcf.gz.tbi"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ }
+}
\ No newline at end of file
--
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