From f169d78589c3e4d2a97892cfc3fb685d6c217d6c Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Tue, 29 Jun 2021 16:02:28 +0200
Subject: [PATCH] add protect
---
hmftools.wdl | 95 ++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 95 insertions(+)
diff --git a/hmftools.wdl b/hmftools.wdl
index f1617bb..646d01e 100644
--- a/hmftools.wdl
+++ b/hmftools.wdl
@@ -542,6 +542,101 @@ task Linx {
}
}
+task Protect {
+ input {
+ String refGenomeVersion
+ String tumorName
+ String normalName
+ Array[String]+ sampleDoids
+ String outputDir = "."
+ Array[File]+ serveActionability
+ File doidsJson
+ File purplePurity
+ File purpleQc
+ File purpleDriverCatalogSomatic
+ File purpleDriverCatalogGermline
+ File purpleSomaticVariants
+ File purpleSomaticVariantsIndex
+ File purpleGermlineVariants
+ File purpleGermlineVariantsIndex
+ File purpleGeneCopyNumber
+ File linxFusion
+ File linxBreakend
+ File linxDriversCatalog
+ File chordPrediction
+ File annotatedVirus
+
+ String memory = "9G"
+ String javaXmx = "8G"
+ Int timeMinutes = 60
+ String dockerImage = "quay.io/biowdl/protect:v1.4"
+ }
+
+ command {
+ protect -Xmx~{javaXmx} \
+ -ref_genome_version ~{refGenomeVersion} \
+ -tumor_sample_id ~{tumorName} \
+ -reference_sample_id ~{normalName} \
+ -primary_tumor_doids ~{sep=";" sampleDoids} \
+ -output_dir ~{outputDir} \
+ -serve_actionability_dir ~{sub(serveActionability[0], basename(serveActionability[0]), "")} \
+ -doid_json ~{doidsJson} \
+ -purple_purity_tsv ~{purplePurity} \
+ -purple_qc_file ~{purpleQc} \
+ -purple_somatic_driver_catalog_tsv ~{purpleDriverCatalogSomatic} \
+ -purple_germline_driver_catalog_tsv ~{purpleDriverCatalogGermline} \
+ -purple_somatic_variant_vcf ~{purpleSomaticVariants} \
+ -purple_germline_variant_vcf ~{purpleGermlineVariants} \
+ -purple_gene_copy_number_tsv ~{purpleGeneCopyNumber} \
+ -linx_fusion_tsv ~{linxFusion} \
+ -linx_breakend_tsv ~{linxBreakend} \
+ -linx_driver_catalog_tsv ~{linxDriversCatalog} \
+ -chord_prediction_txt ~{chordPrediction} \
+ -annotated_virus_tsv ~{annotatedVirus}
+ }
+
+ output {
+ File protectTsv = "~{outputDir}/~{tumorName}.protect.tsv"
+ }
+
+ runtime {
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ memory: memory
+ }
+
+ parameter_meta {
+ refGenomeVersion: {description: "The version of the genome assembly used for alignment. Either \"37\" or \"38\".", category: "required"}
+ tumorName: {description: "The name of the tumor sample.", category: "required"}
+ normalName: {description: "The name of the normal sample.", category: "required"}
+ sampleDoids: {description: "The DOIDs (Human Disease Ontology) for the primary tumor.", category: "required"}
+ outputDir: {description: "The directory the outputs will be written to.", category: "required"}
+ serveActionability: {description: "The actionability files generated by hmftools' serve.", category: "required"}
+ doidsJson: {description: "A json with the DOID (Human Disease Ontology) tree.", category: "required"}
+ purplePurity: {description: "The purity file generated by purple.", category: "required"}
+ purpleQc: {description: "The QC file generated by purple.", category: "required"}
+ purpleDriverCatalogSomatic: {description: "The somatic driver catalog generated by purple.", category: "required"}
+ purpleDriverCatalogGermline: {description: "The germline driver catalog generated by purple.", category: "required"}
+ purpleSomaticVariants: {description: "The somatic VCF generated by purple.", category: "required"}
+ purpleSomaticVariantsIndex: {description: "The index for the somatic VCF generated by purple.", category: "required"}
+ purpleGermlineVariants: {description: "The germline VCF generated by purple.", category: "required"}
+ purpleGermlineVariantsIndex: {description: "The index of the germline VCF generated by purple.", category: "required"}
+ purpleGeneCopyNumber: {description: "The gene copy number file generated by purple.", category: "required"}
+ linxFusion: {description: "The fusion file generated by linx.", category: "required"}
+ linxBreakend: {description: "The breakend file generated by linx.", category: "required"}
+ linxDriversCatalog: {description: "The driver catalog generated generated by linx.", category: "required"}
+ chordPrediction: {description: "The chord prediction file.", category: "required"}
+ annotatedVirus: {description: "The virus-interpreter output.", 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"}
+ }
+}
+
task Purple {
input {
String normalName
--
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