Set working directory for GLNexus docker

BimberLab · Feb 2, 2024 · 3bd8e95 · 3bd8e95
1 parent 70e256b
commit 3bd8e95
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java
@@ -244,6 +244,7 @@ public void execute(List<File> inputGvcfs, File outputVcf, PipelineOutputTracker
                 writer.println("sudo $DOCKER run --rm=true \\");
                 writer.println("\t-v \"${WD}:/work\" \\");
                 writer.println("\t-v \"${HOME}:/homeDir\" \\");
+                writer.println("\t -w /work \\");
                 if (!StringUtils.isEmpty(System.getenv("TMPDIR")))
                 {
                     writer.println("\t-v \"${TMPDIR}:/tmp\" \\");