From 90fd344b8f41fb6b1d632a8412ec2b416c5c7715 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 19 Nov 2020 14:11:19 +0100
Subject: [PATCH] fix some typos
---
hmftools.wdl | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/hmftools.wdl b/hmftools.wdl
index 73c3e31..3757cad 100644
--- a/hmftools.wdl
+++ b/hmftools.wdl
@@ -35,7 +35,7 @@ task Amber {
File referenceFastaDict
Int threads = 2
- String memory = = "33G"
+ String memory = "33G"
String javaXmx = "32G"
Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/hmftools-amber:3.5--0"
@@ -112,7 +112,7 @@ task Cobalt {
File gcProfile
Int threads = 1
- String memory = = "9G"
+ String memory = "9G"
String javaXmx = "8G"
Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/hmftools-cobalt:1.10--0"
@@ -286,10 +286,10 @@ task Purple {
File hotspots
Int threads = 1
- Int time_minutes = 60
+ Int timeMinutes = 60
String memory = "13G"
String javaXmx = "12G"
- String docker = "quay.io/biocontainers/hmftools-purple:2.51--1"
+ String dockerImage = "quay.io/biocontainers/hmftools-purple:2.51--1"
}
command {
@@ -297,8 +297,8 @@ task Purple {
-reference ~{normalName} \
-tumor ~{tumorName} \
-output_dir ~{outputDir} \
- -amber ~{sub(amberOutput, basename(amberOutput[0]), "")} \
- -cobalt ~{sub(cobaltOutput, basename(cobaltOutput[0]), "")} \
+ -amber ~{sub(amberOutput[0], basename(amberOutput[0]), "")} \
+ -cobalt ~{sub(cobaltOutput[0], basename(cobaltOutput[0]), "")} \
-gc_profile ~{gcProfile} \
-somatic_vcf ~{somaticVcf} \
-structural_vcf ~{filteredSvVcf} \
--
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