Fix docker args in GLNexusHandler

BimberLab · Feb 1, 2024 · 00885c7 · 00885c7
1 parent 2407a00
commit 00885c7
Showing 1 changed file with 2 additions and 4 deletions.
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java
@@ -235,20 +235,18 @@ public void execute(List<File> inputGvcfs, File outputVcf, PipelineOutputTracker
                 }
                 writer.println("\t-u $UID \\");
                 writer.println("\t-e USERID=$UID \\");
-                writer.println("\t--entrypoint /bin/bash \\");
-                writer.println("\t-w /work \\");
+
                 Integer maxRam = SequencePipelineService.get().getMaxRam();
                 if (maxRam != null)
                 {
                     writer.println("\t--memory='" + maxRam + "g' \\");
                 }
                 writer.println("\tquay.io/mlin/glnexus:" + binVersion + " \\");
 
-                writer.println("\tglnexus_cli" + " \\");
                 writer.println("\t--config DeepVariant" + " \\");
 
                 gvcfsLocal.forEach(f -> {
-                    writer.println("\t-i gvcf=/work/" + f.getPath() + " \\");
+                    writer.println("\t-i gvcf=/work/" + f.getName() + " \\");
                 });
 
                 Integer maxThreads = SequencePipelineService.get().getMaxThreads(getLogger());