From c522d20e89960242942000c4829ac120825d0cd6 Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 21 Jan 2024 18:28:05 -0800 Subject: [PATCH] Bugfix to DeepVariant docker command --- .../sequenceanalysis/run/analysis/DeepVariantAnalysis.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java index 148c65013..7ce9fc422 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java @@ -204,6 +204,9 @@ private File ensureLocalCopy(File input, File workingDirectory, PipelineOutputTr public void execute(File inputBam, File refFasta, File outputGvcf, PipelineOutputTracker tracker, String binVersion, List extraArgs) throws PipelineJobException { File workDir = outputGvcf.getParentFile(); + File outputVcf = new File(outputGvcf.getPath().replaceAll(".g.vcf", ".vcf")); + tracker.addIntermediateFile(outputVcf); + tracker.addIntermediateFile(new File(outputVcf.getPath() + ".tbi")); File inputBamLocal = ensureLocalCopy(inputBam, workDir, tracker); ensureLocalCopy(SequenceUtil.getExpectedIndex(inputBam), workDir, tracker); @@ -221,6 +224,7 @@ public void execute(File inputBam, File refFasta, File outputGvcf, PipelineOutpu bashArgs.add("--ref=/work/" + refFastaLocal.getName()); bashArgs.add("--reads=/work/" + inputBamLocal.getName()); bashArgs.add("--output_gvcf=/work/" + outputGvcf.getName()); + bashArgs.add("--output_vcf=/work/" + outputVcf.getName()); Integer maxThreads = SequencePipelineService.get().getMaxThreads(getLogger()); if (maxThreads != null) {