From fcc8b13db77e06eb45c00f3ff1d4c3bb2b6dca32 Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 1 Feb 2024 14:01:51 -0800 Subject: [PATCH] Set workDir for DeepVariant/GLNexus --- .../org/labkey/sequenceanalysis/analysis/GLNexusHandler.java | 2 +- .../sequenceanalysis/run/analysis/DeepVariantAnalysis.java | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java index 54d3934a4..3cb14356d 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java @@ -283,7 +283,6 @@ public void execute(List inputGvcfs, File outputVcf, PipelineOutputTracker // Command will fail if this exists: File dbDir = new File (outputVcf.getParentFile(), "GLnexus.DB"); - if (dbDir.exists()) { FileUtils.deleteDirectory(dbDir); @@ -294,6 +293,7 @@ public void execute(List inputGvcfs, File outputVcf, PipelineOutputTracker throw new PipelineJobException(e); } + setWorkingDir(workDir); execute(Arrays.asList("/bin/bash", localBashScript.getPath())); if (!outputVcf.exists()) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java index 06121ab4f..06a5c1b96 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java @@ -284,6 +284,7 @@ public void execute(File inputBam, File refFasta, File outputGvcf, PipelineOutpu throw new PipelineJobException(e); } + setWorkingDir(workDir); execute(Arrays.asList("/bin/bash", localBashScript.getPath())); if (!outputGvcf.exists())