From c2f223eb6a487d7c5bca957bdaaf830d0522d3cb Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Tue, 29 Jun 2021 13:26:01 +0200
Subject: [PATCH] add virusinterpreter
---
hmftools.wdl | 51 +++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 51 insertions(+)
diff --git a/hmftools.wdl b/hmftools.wdl
index 7d6f154..f1617bb 100644
--- a/hmftools.wdl
+++ b/hmftools.wdl
@@ -778,3 +778,54 @@ task Sage {
category: "advanced"}
}
}
+
+task VirusInterpreter {
+ input {
+ String sampleId
+ File virusBreakendTsv
+ File taxonomyDbTsv
+ File virusInterpretationTsv
+ File virusBlacklistTsv
+ String outputDir = "."
+
+ String memory = "3G"
+ String javaXmx = "2G"
+ Int timeMinutes = 15
+ String dockerImage = "quay.io/biowdl/virus-interpreter:1.0"
+ }
+
+ command {
+ virus-interpreter -Xmx~{javaXmx} \
+ -sample_id ~{sampleId} \
+ -virus_breakend_tsv ~{virusBreakendTsv} \
+ -taxonomy_db_tsv ~{taxonomyDbTsv} \
+ -virus_interpretation_tsv ~{virusInterpretationTsv} \
+ -virus_blacklist_tsv ~{virusBlacklistTsv} \
+ -output_dir ~{outputDir}
+ }
+
+ output {
+ File virusAnnotatedTsv = "~{outputDir}/~{sampleId}.virus.annotated.tsv"
+ }
+
+ runtime {
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ memory: memory
+ }
+
+ parameter_meta {
+ sampleId: {description: "The name of the sample.", category: "required"}
+ virusBreakendTsv: {description: "The TSV output from virusbreakend.", category: "required"}
+ taxonomyDbTsv: {description: "A taxonomy database tsv.", category: "required"}
+ virusInterpretationTsv: {description: "A virus interpretation tsv.", category: "required"}
+ virusBlacklistTsv: {description: "A virus blacklist tsv.", category: "required"}
+ outputDir: {description: "The directory the output will be written to.", category: "required"}
+ 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"}
+ }
+}
--
GitLab