From 3ec3131512d26c3564c7fd45122f7636e685caf3 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 24 Jan 2020 14:46:38 +0100
Subject: [PATCH] fix various issues
---
gatk.wdl | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index 9a48ddd..d6b77ff 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -263,7 +263,7 @@ task CallCopyRatioSegments {
command {
set -e
- mkdir -p "$(~{outputPrefix})"
+ mkdir -p "$(dirname ~{outputPrefix})"
gatk --java-options -Xmx~{javaXmx} \
CallCopyRatioSegments \
-I ~{copyRatioSegments} \
@@ -999,15 +999,15 @@ task ModelSegments {
--denoised-copy-ratios ~{denoisedCopyRatios} \
--allelic-counts ~{allelicCounts} \
~{"--normal-allelic-counts " + normalAllelicCounts} \
- --minimum-total-allele-count-case ~{minimumTotalAlleleCountCase}
- --maximum-number-of-smoothing-iterations ~{maximumNumberOfSmoothingIterations}
+ --minimum-total-allele-count-case ~{minimumTotalAlleleCountCase} \
+ --maximum-number-of-smoothing-iterations ~{maximumNumberOfSmoothingIterations} \
--output ~{outputDir} \
--output-prefix ~{outputPrefix}
}
output {
File hetrozygousAllelicCounts = outputDir + "/" + outputPrefix + ".hets.tsv"
- File normalHetrozygousAllelicCounts = outputDir + "/" + outputPrefix + ".hets.normal.tsv"
+ File? normalHetrozygousAllelicCounts = outputDir + "/" + outputPrefix + ".hets.normal.tsv"
File copyRatioSegments = outputDir + "/" + outputPrefix + ".cr.seg"
File copyRatioCBS = outputDir + "/" + outputPrefix + ".cr.igv.seg"
File alleleFractionCBS = outputDir + "/" + outputPrefix + ".af.igv.seg"
@@ -1124,9 +1124,9 @@ task PlotDenoisedCopyRatios {
File standardizedCopyRatios
File denoisedCopyRatios
- String memory = "21G"
+ String memory = "32G"
String javaXmx = "7G"
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "broadinstitute/gatk:4.1.4.0" # The biocontainer doesn't seem to contain R.
}
command {
@@ -1180,13 +1180,13 @@ task PlotModeledSegments {
String memory = "21G"
String javaXmx = "7G"
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "broadinstitute/gatk:4.1.4.0" # The biocontainer doesn't seem to contain R.
}
command {
set -e
mkdir -p ~{outputDir}
- gatk --java-option -Xmx~{javaXmx} \
+ gatk --java-options -Xmx~{javaXmx} \
PlotModeledSegments \
--denoised-copy-ratios ~{denoisedCopyRatios} \
--allelic-counts ~{allelicCounts} \
--
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