From 7d1f9c92406f9865e8c035a5bd19feea5a22b7ae Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Wed, 10 Nov 2021 12:46:04 +0100
Subject: [PATCH] upgrade gridss to 2.12.2
---
gridss.wdl | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/gridss.wdl b/gridss.wdl
index 5c267e7..1f14e23 100644
--- a/gridss.wdl
+++ b/gridss.wdl
@@ -34,7 +34,7 @@ task AnnotateInsertedSequence {
Int threads = 8
String javaXmx = "8G"
String memory = "9G"
- String dockerImage = "quay.io/biocontainers/gridss:2.11.1--hdfd78af_1"
+ String dockerImage = "quay.io/biocontainers/gridss:2.12.2--h270b39a_0"
Int timeMinutes = 120
}
@@ -96,7 +96,7 @@ task GRIDSS {
Int jvmHeapSizeGb = 64
Int threads = 8
Int timeMinutes = ceil(4320 / threads) + 10
- String dockerImage = "quay.io/biocontainers/gridss:2.11.1--hdfd78af_1"
+ String dockerImage = "quay.io/biocontainers/gridss:2.12.2--h270b39a_0"
}
command {
@@ -165,14 +165,14 @@ task GridssAnnotateVcfRepeatmasker {
String memory = "25G"
Int threads = 8
- String dockerImage = "quay.io/biocontainers/gridss:2.11.1--hdfd78af_1"
+ String dockerImage = "quay.io/biocontainers/gridss:2.12.2--h270b39a_0"
Int timeMinutes = 1440
}
command {
gridss_annotate_vcf_repeatmasker \
--output ~{outputPath} \
- --jar /usr/local/share/gridss-2.12.0-1/gridss.jar \
+ --jar /usr/local/share/gridss-2.12.2-0/gridss.jar \
-w . \
-t ~{threads} \
~{gridssVcf}
@@ -213,7 +213,7 @@ task Virusbreakend {
String memory = "75G"
Int threads = 8
- String dockerImage = "quay.io/biocontainers/gridss:2.11.1--hdfd78af_1"
+ String dockerImage = "quay.io/biocontainers/gridss:2.12.2--h270b39a_0"
Int timeMinutes = 180
}
@@ -226,7 +226,7 @@ task Virusbreakend {
--workingdir . \
--reference ~{referenceFasta} \
--db virusbreakenddb \
- --jar /usr/local/share/gridss-2.12.0-1/gridss.jar \
+ --jar /usr/local/share/gridss-2.12.2-0/gridss.jar \
-t ~{threads} \
~{bam}
}
--
GitLab