From 0ec5ac324e41fdb983a88d9b6e1395da9dc9fff2 Mon Sep 17 00:00:00 2001
From: cedrick <cagaser@outlook.com>
Date: Mon, 10 Feb 2020 14:20:33 +0100
Subject: [PATCH] minor fix
---
clever.wdl | 4 ++--
manta.wdl | 6 +++---
picard.wdl | 2 +-
3 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/clever.wdl b/clever.wdl
index 34a9612..54f8108 100644
--- a/clever.wdl
+++ b/clever.wdl
@@ -1,5 +1,5 @@
version 1.0
-
+import "bwa.wdl"
task Prediction {
input {
File bamFile
@@ -30,7 +30,7 @@ task Prediction {
runtime {
cpu: threads
- memory: mem
+ memory: memory
docker: dockerImage
}
diff --git a/manta.wdl b/manta.wdl
index 4b970fb..09a7c4e 100644
--- a/manta.wdl
+++ b/manta.wdl
@@ -88,7 +88,7 @@ task Germline {
Boolean exome = false
Int cores = 1
- String memory = "4G"
+ Int memoryGb = 4
}
command {
@@ -103,7 +103,7 @@ task Germline {
~{runDir}/runWorkflow.py \
-m local \
-j ~{cores} \
- -g ~{memory}
+ -g ~{memoryGb}
}
output {
@@ -113,7 +113,7 @@ task Germline {
runtime {
cpu: cores
- memory: memory
+ memory: "~{memoryGb}G"
docker: dockerImage
}
}
diff --git a/picard.wdl b/picard.wdl
index 4abd7ce..cd923bb 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -638,7 +638,7 @@ task RenameSample {
runtime {
docker: dockerImage
- memory = memory
+ memory: memory
}
}
--
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