From c8af9b5de589c3aaceb7d9096090c1cd581e3616 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 19 Feb 2019 16:45:57 +0100
Subject: [PATCH] dockerize scatterregions
---
biopet/biopet.wdl | 11 +++--------
1 file changed, 3 insertions(+), 8 deletions(-)
diff --git a/biopet/biopet.wdl b/biopet/biopet.wdl
index 310d9c0..8a66e42 100644
--- a/biopet/biopet.wdl
+++ b/biopet/biopet.wdl
@@ -235,27 +235,21 @@ task ReorderGlobbedScatters {
task ScatterRegions {
input {
- String? preCommand
Reference reference
String outputDirPath
- File? toolJar
Int? scatterSize
File? regions
Boolean notSplitContigs = false
Int memory = 4
Float memoryMultiplier = 3.0
+ String dockerTag = "0.2--0"
}
- String toolCommand = if defined(toolJar)
- then "java -Xmx" + memory + "G -jar " +toolJar
- else "biopet-scatterregions -Xmx" + memory + "G"
-
command {
set -e -o pipefail
- ~{preCommand}
mkdir -p ~{outputDirPath}
- ~{toolCommand} \
+ biopet-scatterregions -Xmx~{memory}G \
-R ~{reference.fasta} \
-o ~{outputDirPath} \
~{"-s " + scatterSize} \
@@ -268,6 +262,7 @@ task ScatterRegions {
}
runtime {
+ docker: "quay.io/biopet-scatterregions/gatk:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
--
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