From f2cc5cc02fb5ed2376969ff745ce0d6741fc32ff Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 25 Feb 2022 11:43:22 +0100
Subject: [PATCH] add LinxVisualisations
---
hmftools.wdl | 55 ++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 55 insertions(+)
diff --git a/hmftools.wdl b/hmftools.wdl
index 9a3bd43..c852b52 100644
--- a/hmftools.wdl
+++ b/hmftools.wdl
@@ -622,6 +622,61 @@ task Linx {
}
}
+task LinxVisualisations {
+ input {
+ String outputDir = "./linx_visualisation"
+ String sample
+ String refGenomeVersion
+ Array[File]+ linxOutput
+ Boolean plotReportable = true
+
+ String memory = "9G"
+ String javaXmx = "8G"
+ Int timeMinutes = 10
+ String dockerImage = "quay.io/biocontainers/hmftools-linx:1.18--hdfd78af_0"
+ }
+
+ command {
+ set -e
+ mkdir -p ~{outputDir}
+ java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+ -cp /usr/local/share/hmftools-linx-1.18-0/sv-linx.jar \
+ com.hartwig.hmftools.linx.visualiser.SvVisualiser \
+ -sample ~{sample} \
+ -ref_genome_version ~{refGenomeVersion} \
+ -circos /usr/local/bin/circos \
+ -vis_file_dir ~{sub(linxOutput[0], basename(linxOutput[0]), "")} \
+ -data_out ~{outputDir}/circos \
+ -plot_out ~{outputDir}/plot \
+ ~{if plotReportable then "-plot_reportable" else ""}
+ }
+
+ output {
+
+ }
+
+ runtime {
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ memory: memory
+ }
+
+ parameter_meta {
+ outputDir: {description: "The directory the outputs will be written to.", category: "required"}
+ sample: {description: "The sample's name.", category: "required"}
+ refGenomeVersion: {description: "The version of the genome assembly used for alignment. Either \"37\" or \"38\".", category: "required"}
+ linxOutput: {description: "The directory containing the linx output.", category: "required"}
+ plotReportable: {description: "Equivalent to the -plot_reportable flag.", category: "advanced"}
+
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ 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"}
+ }
+}
+
task Pave {
input {
String outputDir = "./"
--
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