From 743acb0b89cc4893544965e3d93590978b414420 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Tue, 1 Jun 2021 12:13:09 +0200
Subject: [PATCH] Fix memory values.
---
CHANGELOG.md | 1 +
CPAT.wdl | 5 ++++-
gffcompare.wdl | 3 +++
gffread.wdl | 3 +++
4 files changed, 11 insertions(+), 1 deletion(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 28e998e..e47033c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ that users understand how the changes affect the new version.
version 5.0.0-dev
---------------------------
++ Add memory values to GffCompare, GffRead and CPAT.
+ GffCompare: Make the `referenceAnnotation` input optional.
+ Stringtie: Add the `minimumCoverage` input.
+ UMI-tools: update default dockerImage to use umitools v1.1.1 with correct samtools version (1.10)
diff --git a/CPAT.wdl b/CPAT.wdl
index afb6785..4a6d447 100644
--- a/CPAT.wdl
+++ b/CPAT.wdl
@@ -34,6 +34,7 @@ task CPAT {
Array[String]? startCodons
Array[String]? stopCodons
+ String memory = "4G"
Int timeMinutes = 10 + ceil(size(gene, "G") * 30)
String dockerImage = "biocontainers/cpat:v1.2.4_cv1"
}
@@ -60,8 +61,9 @@ task CPAT {
}
runtime {
- docker: dockerImage
+ memory: memory
time_minutes: timeMinutes
+ docker: dockerImage
}
parameter_meta {
@@ -74,6 +76,7 @@ task CPAT {
referenceGenomeIndex: {description: "The index of the reference. Should be added as input if CPAT should not index the reference genome.", category: "advanced"}
startCodons: {description: "Equivalent to CPAT's `--start` option.", category: "advanced"}
stopCodons: {description: "Equivalent to CPAT's `--stop` option.", category: "advanced"}
+ memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
diff --git a/gffcompare.wdl b/gffcompare.wdl
index 5c83ba9..aa7c720 100644
--- a/gffcompare.wdl
+++ b/gffcompare.wdl
@@ -46,6 +46,7 @@ task GffCompare {
Int? maxDistanceGroupingTranscriptStartSites
String? namePrefix
+ String memory = "4G"
Int timeMinutes = 1 + ceil(size(inputGtfFiles, "G") * 30)
String dockerImage = "quay.io/biocontainers/gffcompare:0.10.6--h2d50403_0"
@@ -114,6 +115,7 @@ task GffCompare {
}
runtime {
+ memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
@@ -140,6 +142,7 @@ task GffCompare {
maxDistanceFreeEndsTerminalExons: {description: "Equivalent to gffcompare's `-e` option.", category: "advanced"}
maxDistanceGroupingTranscriptStartSites: {description: "Equivalent to gffcompare's `-d` option.", category: "advanced"}
namePrefix: {description: "Equivalent to gffcompare's `-p` option.", category: "advanced"}
+ memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
diff --git a/gffread.wdl b/gffread.wdl
index 967dd5c..a04540f 100644
--- a/gffread.wdl
+++ b/gffread.wdl
@@ -32,6 +32,7 @@ task GffRead {
String? proteinFastaPath
String? filteredGffPath
+ String memory = "4G"
Int timeMinutes = 1 + ceil(size(inputGff, "G") * 10)
String dockerImage = "quay.io/biocontainers/gffread:0.9.12--0"
}
@@ -64,6 +65,7 @@ task GffRead {
}
runtime {
+ memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
@@ -78,6 +80,7 @@ task GffRead {
CDSFastaPath: {description: "The location the CDS fasta should be written to.", category: "advanced"}
proteinFastaPath: {description: "The location the protein fasta should be written to.", category: "advanced"}
filteredGffPath: {description: "The location the filtered GFF should be written to.", category: "advanced"}
+ memory: {description: "The amount of memory available to the job.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
--
GitLab