From d5294222e69c6e793ea0d13e448e67b9482e5a10 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 3 Mar 2022 15:50:52 +0100
Subject: [PATCH] add orange, cupGenerateReport and (hopefully) fix sage plots
---
hmftools.wdl | 212 ++++++++++++++++++++++++++++++++++++++++++++++++++-
1 file changed, 208 insertions(+), 4 deletions(-)
diff --git a/hmftools.wdl b/hmftools.wdl
index 277c8dd..75fd2d1 100644
--- a/hmftools.wdl
+++ b/hmftools.wdl
@@ -168,6 +168,62 @@ task Cobalt {
}
}
+task CupGenerateReport {
+ input {
+ String sampleName
+ File cupData
+ String outputDir = "./cuppa"
+
+ String memory = "5G"
+ Int timeMinutes = 10
+ String dockerImage = "quay.io/biowdl/cuppa:1.6"
+ }
+
+ # This script writes to the directory that the input is located in.
+ # Giving the input directly will cause the script to write in the
+ # locallized input dir, which may cause issues with write permissions
+ # in certain execution engines or backends. We, therefore, make links
+ # to a working directory, and give that directory as input instead.
+ # We can't just use the outputDir directly. This could be an
+ # absolute path in which case the linking might fail due to name
+ # collisions. Outputs are copied to the given output dir afterwards.
+ command {
+ set -e
+ mkdir -p ./workdir ~{outputDir}
+ ln -s -t workdir ~{sep=" " cupData}
+ CupGenerateReport \
+ ~{sampleName} \
+ workdir
+ mv -t ~{outputDir} \
+ ./workdir/~{sampleName}.cup.report.summry.png \
+ ./workdir/~{sampleName}.cup.report.features.png \
+ ./workdir/~{sampleName}_cup.report.pdf
+ }
+
+ output {
+ File summaryPng = "~{outputDir}/~{sampleName}.cup.report.summry.png"
+ File featuresPng = "~{outputDir}/~{sampleName}.cup.report.features.png"
+ File reportPdf = "~{outputDir}/~{sampleName}_cup.report.pdf"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ sampleName: {description: "The sample id.", category: "required"}
+ cupData: {description: "The output produced by cuppa.", category: "required"}
+ outputDir: {description: "The directory the ouput will be placed in.", category: "common"}
+
+ memory: {description: "The amount of memory this job will 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"}
+ }
+}
+
task Cuppa {
input {
Array[File]+ linxOutput
@@ -632,7 +688,7 @@ task LinxVisualisations {
String memory = "9G"
String javaXmx = "8G"
- Int timeMinutes = 1440 #FIXME
+ Int timeMinutes = 1440
String dockerImage = "quay.io/biocontainers/hmftools-linx:1.18--hdfd78af_0"
}
@@ -678,6 +734,151 @@ task LinxVisualisations {
}
}
+task Orange {
+ input {
+ String outputDir = "./orange"
+ File doidJson
+ Array[String] sampleDoids
+ String tumorName
+ String referenceName
+ File referenceMetrics
+ File tumorMetrics
+ File referenceFlagstats
+ File tumorFlagstats
+ File sageGermlineGeneCoverageTsv
+ File sageSomaticRefSampleBqrPlot
+ File sageSomaticTumorSampleBqrPlot
+ File purpleGeneCopyNumberTsv
+ File purpleGermlineDriverCatalogTsv
+ File purpleGermlineVariantVcf
+ File purpleGermlineVariantVcfIndex
+ Array[File]+ purplePlots
+ File purplePurityTsv
+ File purpleQcFile
+ File purpleSomaticDriverCatalogTsv
+ File purpleSomaticVariantVcf
+ File purpleSomaticVariantVcfIndex
+ File linxFusionTsv
+ File linxBreakendTsv
+ File linxDriverCatalogTsv
+ File linxDriverTsv
+ Array[File]+ linxPlots
+ File cuppaResultCsv
+ File cuppaSummaryPlot
+ File cuppaFeaturePlot
+ File chordPredictionTxt
+ File peachGenotypeTsv
+ File protectEvidenceTsv
+ File annotatedVirusTsv
+ #File pipelineVersionFile
+ File cohortMappingTsv
+ File cohortPercentilesTsv
+
+ String memory = "17G"
+ String javaXmx = "16G"
+ Int timeMinutes = 1440 #FIXME
+ String dockerImage = "quay.io/biocontainers/hmftools-linx:1.18--hdfd78af_0"
+ }
+
+ command {
+ set -e
+ mkdir -p ~{outputDir}
+ orange -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+ -output_dir ~{outputDir} \
+ -doid_json ~{doidJson} \
+ -primary_tumor_doids '~{sep=";" sampleDoids}' \
+ -max_evidence_level C \
+ -tumor_sample_id ~{tumorName} \
+ -reference_sample_id ~{referenceName} \
+ -ref_sample_wgs_metrics_file ~{referenceMetrics} \
+ -tumor_sample_wgs_metrics_file ~{tumorMetrics} \
+ -ref_sample_flagstat_file ~{referenceFlagstats} \
+ -tumor_sample_flagstat_file ~{tumorFlagstats} \
+ -sage_germline_gene_coverage_tsv ~{sageGermlineGeneCoverageTsv} \
+ -sage_somatic_ref_sample_bqr_plot ~{sageSomaticRefSampleBqrPlot} \
+ -sage_somatic_tumor_sample_bqr_plot ~{sageSomaticTumorSampleBqrPlot} \
+ -purple_gene_copy_number_tsv ~{purpleGeneCopyNumberTsv} \
+ -purple_germline_driver_catalog_tsv ~{purpleGermlineDriverCatalogTsv} \
+ -purple_germline_variant_vcf ~{purpleGermlineVariantVcf} \
+ -purple_plot_directory ~{sub(purplePlots[0], basename(purplePlots[0]), "")} \
+ -purple_purity_tsv ~{purplePurityTsv} \
+ -purple_qc_file ~{purpleQcFile} \
+ -purple_somatic_driver_catalog_tsv ~{purpleSomaticDriverCatalogTsv} \
+ -purple_somatic_variant_vcf ~{purpleSomaticVariantVcf} \
+ -linx_fusion_tsv ~{linxFusionTsv} \
+ -linx_breakend_tsv ~{linxBreakendTsv} \
+ -linx_driver_catalog_tsv ~{linxDriverCatalogTsv} \
+ -linx_driver_tsv ~{linxDriverTsv} \
+ -linx_plot_directory ~{sub(linxPlots[0], basename(linxPlots[0]), "")} \
+ -cuppa_result_csv ~{cuppaResultCsv} \
+ -cuppa_summary_plot ~{cuppaSummaryPlot} \
+ -cuppa_feature_plot ~{cuppaFeaturePlot} \
+ -chord_prediction_txt ~{chordPredictionTxt} \
+ -peach_genotype_tsv ~{peachGenotypeTsv} \
+ -protect_evidence_tsv ~{protectEvidenceTsv} \
+ -annotated_virus_tsv ~{annotatedVirusTsv} \
+ -cohort_mapping_tsv ~{cohortMappingTsv} \
+ -cohort_percentiles_tsv ~{cohortPercentilesTsv}
+ }
+ #TODO may need to be added: -pipeline_version_file ~{pipelineVersionFile}
+
+ output {
+ File orangeJson = "~{outputDir}/~{tumorName}.orange.json"
+ File orangePdf = "~{outputDir}/~{tumorName}.orange.pdf"
+ }
+
+ runtime {
+ time_minutes: timeMinutes # !UnknownRuntimeKey
+ docker: dockerImage
+ memory: memory
+ }
+
+ parameter_meta {
+ outputDir: {description: "The directory the outputs will be written to.", category: "common"}
+ doidJson: {description: "A json with the DOID (Human Disease Ontology) tree.", category: "required"}
+ sampleDoids: {description: "The DOIDs (Human Disease Ontology) for the primary tumor.", category: "required"}
+ tumorName: {description: "The name of the tumor sample.", category: "required"}
+ referenceName: {description: "The name of the normal sample.", category: "required"}
+ referenceMetrics: {description: "The picard WGS metrics for the normal sample.", category: "required"}
+ tumorMetrics: {description: "The picard WGS metrics for the tumor sample.", category: "required"}
+ referenceFlagstats: {description: "The flagstats for the normal sample.", category: "required"}
+ tumorFlagstats: {description: "The flagstats for the tumor sample.", category: "required"}
+ sageGermlineGeneCoverageTsv: {description: "Gene coverage file produced by the germline sage run.", category: "required"}
+ sageSomaticRefSampleBqrPlot: {description: "The reference bqr plot produced by the somatic sage run.", category: "required"}
+ sageSomaticTumorSampleBqrPlot: {description: "The reference bqr plot produced by the somatic sage run.", category: "required"}
+ purpleGeneCopyNumberTsv: {description: "Copy number tsv produced by purple.", category: "required"}
+ purpleGermlineDriverCatalogTsv: {description: "Germline driver catalog produced by purple.", category: "required"}
+ purpleGermlineVariantVcf: {description: "Germline variant vcf produced by purple.", category: "required"}
+ purplePlots: {description: "The plots generated by purple.", category: "required"}
+ purplePurityTsv: {description: "The purity file produced by purple.", category: "required"}
+ purpleQcFile: {description: "The qc file produced by purple.", category: "required"}
+ purpleSomaticDriverCatalogTsv: {description: "Somatic driver catalog produced by purple.", category: "required"}
+ purpleSomaticVariantVcf: {description: "Somatic variant vcf produced by purple.", category: "required"}
+ linxFusionTsv: {description: "The fusions tsv produced by linx.", category: "required"}
+ linxBreakendTsv: {description: "The breakend tsv produced by linx.", category: "required"}
+ linxDriverCatalogTsv: {description: "The driver catalog produced by linx.", category: "required"}
+ linxDriverTsv: {description: "The driver tsv produced by linx.", category: "required"}
+ linxPlots: {description: "The plots generated by linx.", category: "required"}
+ cuppaResultCsv: {description: "The cuppa results csv.", category: "required"}
+ cuppaSummaryPlot: {description: "The cuppa summary plot.", category: "required"}
+ cuppaFeaturePlot: {description: "The cuppa feature plot.", category: "required"}
+ chordPredictionTxt: {description: "Chord prediction results.", category: "required"}
+ peachGenotypeTsv: {description: "Genotype tsv produced by peach.", category: "required"}
+ protectEvidenceTsv: {description: "Evidence tsv produced by protect.", category: "required"}
+ annotatedVirusTsv: {description: "Annotated virus tsv produced by virus-interpreter.", category: "required"}
+ #pipelineVersionFile: {description: "", category: "required"}
+ cohortMappingTsv: {description: "Cohort mapping file from the HMFTools resources.", category: "required"}
+ cohortPercentilesTsv: {description: "Cohort percentile file from the HMFTools resources.", 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 Pave {
input {
String outputDir = "./"
@@ -1024,7 +1225,7 @@ task Sage {
String javaXmx = "50G"
String memory = "51G"
Int timeMinutes = 1 + ceil(size(select_all([tumorBam, referenceBam]), "G") * 9 / threads)
- String dockerImage = "quay.io/biocontainers/hmftools-sage:2.8--hdfd78af_0"
+ String dockerImage = "quay.io/biocontainers/hmftools-sage:2.8--hdfd78af_1"
}
command {
@@ -1054,8 +1255,11 @@ task Sage {
output {
File outputVcf = outputPath
File outputVcfIndex = outputPath + ".tbi"
- # There is some plots as well, but in the current container the labels in the plots are just series of `â–¡`s.
- # This seems to be a systemic issue with R generated plots in biocontainers...
+ File? referenceSageBqrPng = "~{referenceName}.sage.bqr.png"
+ File? referenceSageBqrTsv = "~{referenceName}.sage.bqr.tsv"
+ File tumorSageBqrPng = "~{tumorName}.sage.bqr.png"
+ File tumorSageBqrTsv = "~{tumorName}.sage.bqr.tsv"
+ File sageGeneCoverageTsv = "~{tumorName}.sage.gene.coverage.tsv"
}
runtime {
--
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