From 04c65ab38a2d91051e3c0aa90c67738b755a4921 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Mon, 28 Jun 2021 15:29:21 +0200
Subject: [PATCH] add virusbreakend
---
gridss.wdl | 63 ++++++++++++++++++++++++++++++++++++++++++++++++++++--
1 file changed, 61 insertions(+), 2 deletions(-)
diff --git a/gridss.wdl b/gridss.wdl
index 3844c60..52e039d 100644
--- a/gridss.wdl
+++ b/gridss.wdl
@@ -164,7 +164,7 @@ task GridssAnnotateVcfRepeatmasker {
String memory = "4G"
String dockerImage = "quay.io/biocontainers/gridss:2.12.0--h270b39a_1"
- Int timeMinutes = 1 + ceil(size(inputVcf, "G") * 3)
+ Int timeMinutes = 1 + ceil(size(gridssVcf, "G") * 3)
}
command {
@@ -181,6 +181,12 @@ task GridssAnnotateVcfRepeatmasker {
}
runtime {
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
gridssVcf: {description: "The GRIDSS output.", category: "required"}
gridssVcfIndex: {description: "The index for the GRIDSS output.", category: "required"}
outputPath: {description: "The path the output should be written to.", category: "common"}
@@ -189,4 +195,57 @@ task GridssAnnotateVcfRepeatmasker {
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"}
}
-}
\ No newline at end of file
+}
+
+task Virusbreakend {
+ input {
+ File bam
+ File bamIndex
+ File referenceFasta
+ File virusbreakendDB
+ String outputPath = "./virusbreakend.vcf"
+
+ String memory = "75G"
+ Int threads = 8
+ String dockerImage = "quay.io/biocontainers/gridss:2.12.0--h270b39a_1"
+ Int timeMinutes = 180
+ }
+
+ command {
+ mkdir virusbreakenddb
+ tar -xzvf ~{virusbreakendDB} -C virusbreakenddb --strip-components 1
+ virusbreakend \
+ --output ~{outputPath} \
+ --workingdir . \
+ --reference ~{referenceFasta} \
+ --db virusbreakenddb \
+ --jar /usr/local/share/gridss-2.12.0-1/gridss.jar \
+ -t ~{threads} \
+ ~{bam}
+ }
+
+ output {
+ File vcf = outputPath
+ File summary = "~{outputPath}.summary.tsv"
+ }
+
+ runtime {
+ cpu: threads
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ bam: {description: "A BAM file.", category: "required"}
+ bamIndex: {description: "The index for the BAM file.", category: "required"}
+ referenceFasta: {description: "The fasta of the reference genome.", category: "required"}
+ virusbreakendDB: {description: "A .tar.gz containing the virusbreakend database.", category: "required"}
+ outputPath: {description: "The path the output should be written to.", category: "common"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ threads: {description: "The number of the threads to use.", 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"}
+ }
+}
--
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