From 4f31b5fb1b6af42941545ee54b862ff74e6d7373 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 9 Jun 2020 15:40:40 +0200
Subject: [PATCH] allow for very large scattersizes
---
biopet/biopet.wdl | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/biopet/biopet.wdl b/biopet/biopet.wdl
index cc8e1bc..8931940 100644
--- a/biopet/biopet.wdl
+++ b/biopet/biopet.wdl
@@ -214,6 +214,7 @@ task ScatterRegions {
input {
File referenceFasta
File referenceFastaDict
+ Int scatterSizeMillions = 1000
Int? scatterSize
File? regions
Boolean notSplitContigs = false
@@ -230,6 +231,7 @@ task ScatterRegions {
# linking. This path must be in the containers filesystem, otherwise the
# linking does not work.
String outputDirPath = "scatters"
+ String finalSize = if defined(scatterSize) then "~{scatterSize}" else "~{scatterSizeMillions}000000"
command <<<
set -e -o pipefail
@@ -237,7 +239,7 @@ task ScatterRegions {
biopet-scatterregions -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
-R ~{referenceFasta} \
-o ~{outputDirPath} \
- ~{"-s " + scatterSize} \
+ ~{"-s " + finalSize} \
~{"-L " + regions} \
~{"--bamFile " + bamFile} \
~{true="--notSplitContigs" false="" notSplitContigs}
@@ -271,7 +273,8 @@ task ScatterRegions {
referenceFasta: {description: "The reference fasta file.", category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
category: "required"}
- scatterSize: {description: "Equivalent to biopet scatterregions' `-s` option.", category: "common"}
+ scatterSizeMillions: {description: "Over how many million base pairs should be scattered.", category: "common"}
+ scatterSize: {description: "Overrides scatterSizeMillions with a smaller value if set.", category: "advanced"}
regions: {description: "The regions to be scattered.", category: "advanced"}
notSplitContigs: {description: "Equivalent to biopet scatterregions' `--notSplitContigs` flag.",
category: "advanced"}
--
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