From eac2b302158e412df419705eba39ebaeedc1c11f Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Tue, 9 Feb 2021 16:10:52 +0100
Subject: [PATCH] small adjustments
---
bwa.wdl | 4 +++-
gridss.wdl | 6 +++---
hmftools.wdl | 12 ++++++------
sambamba.wdl | 2 +-
4 files changed, 13 insertions(+), 11 deletions(-)
diff --git a/bwa.wdl b/bwa.wdl
index 203f0dd..e239348 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -28,6 +28,7 @@ task Mem {
String outputPrefix
Boolean sixtyFour = false
Boolean usePostalt = false
+ Boolean useSoftclippingForSupplementary = false
Int sortMemoryPerThreadGb = 2
Int compressionLevel = 1
@@ -36,7 +37,7 @@ task Mem {
Int threads = 4
Int? memoryGb
- Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 260 / threads)
+ Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 500 / threads)
# Contains bwa 0.7.17 bwakit 0.7.17.dev1 and samtools 1.10.
String dockerImage = "quay.io/biocontainers/mulled-v2-ad317f19f5881324e963f6a6d464d696a2825ab6:c59b7a73c87a9fe81737d5d628e10a3b5807f453-0"
}
@@ -56,6 +57,7 @@ task Mem {
mkdir -p "$(dirname ~{outputPrefix})"
bwa mem \
-t ~{threads} \
+ ~{if useSoftclippingForSupplementary then "-Y" else ""} \
~{"-R '" + readgroup}~{true="'" false="" defined(readgroup)} \
~{bwaIndex.fastaFile} \
~{read1} \
diff --git a/gridss.wdl b/gridss.wdl
index 9bafa6d..0148fcf 100644
--- a/gridss.wdl
+++ b/gridss.wdl
@@ -35,9 +35,9 @@ task GRIDSS {
String? normalLabel
Int jvmHeapSizeGb = 30
- Int threads = 2
- Int timeMinutes = ceil(2880 / threads) + 10
- String dockerImage = "quay.io/biocontainers/gridss:2.9.4--0"
+ Int threads = 4
+ Int timeMinutes = ceil(5760 / threads) + 10
+ String dockerImage = "quay.io/biocontainers/gridss:2.9.3--0"
}
command {
diff --git a/hmftools.wdl b/hmftools.wdl
index 5bad1db..9056406 100644
--- a/hmftools.wdl
+++ b/hmftools.wdl
@@ -181,13 +181,13 @@ task GripssApplicationKt {
String memory = "25G"
String javaXmx = "24G"
- Int timeMinutes = 60
- String dockerImage = "quay.io/biocontainers/hmftools-gripss:1.8--0"
+ Int timeMinutes = 120
+ String dockerImage = "quay.io/biocontainers/hmftools-gripss:1.7--0"
}
command {
java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
- -cp /usr/local/share/hmftools-gripss-1.8-0/gripss.jar \
+ -cp /usr/local/share/hmftools-gripss-1.7-0/gripss.jar \
com.hartwig.hmftools.gripss.GripssApplicationKt \
-ref_genome ~{referenceFasta} \
-breakpoint_hotspot ~{breakpointHotspot} \
@@ -234,13 +234,13 @@ task GripssHardFilterApplicationKt {
String memory = "25G"
String javaXmx = "24G"
- Int timeMinutes = 60
- String dockerImage = "quay.io/biocontainers/hmftools-gripss:1.8--0"
+ Int timeMinutes = 120
+ String dockerImage = "quay.io/biocontainers/hmftools-gripss:1.7--0"
}
command {
java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
- -cp /usr/local/share/hmftools-gripss-1.8-0/gripss.jar \
+ -cp /usr/local/share/hmftools-gripss-1.7-0/gripss.jar \
com.hartwig.hmftools.gripss.GripssHardFilterApplicationKt \
-input_vcf ~{inputVcf} \
-output_vcf ~{outputPath}
diff --git a/sambamba.wdl b/sambamba.wdl
index bb63f66..5284363 100644
--- a/sambamba.wdl
+++ b/sambamba.wdl
@@ -84,7 +84,7 @@ task Markdup {
# Added 1024 mb as a margin of safety. Real life use with this setting uses 2.7 GiB.
Int memoryMb = 1024 + sortBufferSize + 2 * ioBufferSize
# Time minute calculation does not work well for higher number of threads.
- Int timeMinutes = 1 + ceil(size(inputBams, "G") * 16) / threads
+ Int timeMinutes = 1 + ceil(size(inputBams, "G") * 32) / threads
String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
}
--
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