From b7e9ca35be24be4887fb9b45b7a0d8cfd0a14a9e Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Wed, 12 Jun 2019 13:45:02 +0200
Subject: [PATCH] memory adjustments
---
biopet/biopet.wdl | 2 +-
cutadapt.wdl | 2 +-
htseq.wdl | 2 +-
picard.wdl | 10 +++++-----
4 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/biopet/biopet.wdl b/biopet/biopet.wdl
index 149d8bf..52180b8 100644
--- a/biopet/biopet.wdl
+++ b/biopet/biopet.wdl
@@ -84,7 +84,7 @@ task ExtractAdaptersFastqc {
Float? adapterCutoff
Boolean? outputAsFasta
- Int memory = 4
+ Int memory = 8
Float memoryMultiplier = 5 # This is ridiculous...
String dockerTag = "0.2--1"
}
diff --git a/cutadapt.wdl b/cutadapt.wdl
index 9b3f4a9..cf9095b 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -62,7 +62,7 @@ task Cutadapt {
String? reportPath
Int cores = 1
- Int memory = 8
+ Int memory = 16
String dockerTag = "2.3--py36h14c3975_0"
}
diff --git a/htseq.wdl b/htseq.wdl
index 3011c36..b084709 100644
--- a/htseq.wdl
+++ b/htseq.wdl
@@ -10,7 +10,7 @@ task HTSeqCount {
String order = "pos"
String stranded = "no"
- Int memory = 20
+ Int memory = 40
String dockerTag = "0.9.1--py36h7eb728f_2"
}
diff --git a/picard.wdl b/picard.wdl
index 2628ca8..9f42acb 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -50,8 +50,8 @@ task CollectMultipleMetrics {
Boolean collectSequencingArtifactMetrics = true
Boolean collectQualityYieldMetrics = true
- Int memory = 4
- Float memoryMultiplier = 3.5
+ Int memory = 8
+ Float memoryMultiplier = 4
String dockerTag = "8dde04faba6c9ac93fae7e846af3bafd2c331b3b-0"
}
@@ -133,8 +133,8 @@ task CollectRnaSeqMetrics {
String basename
String strandSpecificity = "NONE"
- Int memory = 4
- Float memoryMultiplier = 3.0
+ Int memory = 8
+ Float memoryMultiplier = 4.0
String dockerTag = "8dde04faba6c9ac93fae7e846af3bafd2c331b3b-0"
}
@@ -278,7 +278,7 @@ task MarkDuplicates {
String outputBamPath
String metricsPath
- Int memory = 4
+ Int memory = 8
Float memoryMultiplier = 3.0
String dockerTag = "2.18.26--0"
--
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