From e01a682ccf993792dd328d34b50611dfec239ae4 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 26 Sep 2018 13:27:29 +0200
Subject: [PATCH] Added CaseControl tool
---
biopet/sampleconfig.wdl | 40 ++++++++++++++++++++++++++++++++++++++++
common.wdl | 7 +++++++
2 files changed, 47 insertions(+)
diff --git a/biopet/sampleconfig.wdl b/biopet/sampleconfig.wdl
index 61defae..dacf47e 100644
--- a/biopet/sampleconfig.wdl
+++ b/biopet/sampleconfig.wdl
@@ -1,5 +1,7 @@
version 1.0
+import "../common.wdl" as common
+
task SampleConfig {
input {
File? toolJar
@@ -77,3 +79,41 @@ task SampleConfigCromwellArrays {
memory: ceil(memory * memoryMultiplier)
}
}
+
+task CaseControl {
+ input {
+ File? toolJar
+ String? preCommand
+ Array[File]+ inputFiles
+ Array[File]+ sampleConfigs
+ String outputPath
+ String controlTag = "control"
+
+ Int memory = 4
+ Float memoryMultiplier = 1.5
+ }
+
+ String toolCommand = if defined(toolJar)
+ then "java -Xmx" + memory + "G -jar " + toolJar
+ else "biopet-sampleconfig -Xmx" + memory + "G"
+
+ command {
+ set -e -o pipefail
+ ~{preCommand}
+ mkdir -p $(dirname ~{outputPath})
+ ~{toolCommand} CromwellArrays \
+ -i ~{sep="-i " inputFiles} \
+ -s ~{sep="-s " inputFiles} \
+ ~{"-o " + outputPath} \
+ ~{"--controlTag " + controlTag}
+ }
+
+ output {
+ File outputFile = outputPath
+ Array[CaseControl] controls = read_json(outputFile)
+ }
+
+ runtime {
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
diff --git a/common.wdl b/common.wdl
index af3b66b..c618cbf 100644
--- a/common.wdl
+++ b/common.wdl
@@ -163,3 +163,10 @@ struct FastqPair {
File? R2
File? R2_md5
}
+
+struct CaseControl {
+ String inputName
+ IndexedBamFile inputBam
+ String controlName
+ IndexedBamFile controlBam
+}
--
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