From 789d3240ae31cc3950c8c82d079f249498011035 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B3nio=20Paulo?= <antonio.do.paulo@ist.utl.pt>
Date: Thu, 1 Aug 2019 17:43:29 +0200
Subject: [PATCH] add GATK GetPileupSummaries as a task
---
gatk.wdl | 35 +++++++++++++++++++++++++++++++++++
1 file changed, 35 insertions(+)
diff --git a/gatk.wdl b/gatk.wdl
index 6d05cb9..efa9bb8 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -354,6 +354,41 @@ task MergeStats {
}
}
+task GetPileupSummaries {
+ input {
+ String sampleName
+ File sampleBam
+ File sampleBamIndex
+ File variantsForContamination
+ File variantsForContaminationIndex
+ File sitesForContamination
+ File sitesForContaminationIndex
+
+ Int memory = 4
+ Float memoryMultiplier = 1.5
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
+ }
+
+ command {
+ set -e
+ gatk --java-options -Xmx~{memory}G \
+ GetPileupSummaries \
+ -I ~{sampleBam} \
+ -V ~{variantsForContamination} \
+ -L ~{sitesForContamination} \
+ -O ~{sampleName + "-pileups.table"}
+ }
+
+ output {
+ File pileups = sampleName + "-pileups.table"
+ }
+
+ runtime {
+ docker: dockerImage
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
+
task SplitNCigarReads {
input {
File inputBam
--
GitLab