Remove -S from fasterq-dump

BimberLab · Jan 13, 2025 · 892c793 · 892c793
1 parent 333d25b
commit 892c793
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Showing 2 changed files with 3 additions and 1 deletion.
diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/DockerWrapper.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/DockerWrapper.java
@@ -109,6 +109,8 @@ public void executeWithDocker(List<String> containerArgs, File workDir, Pipeline
 
             writer.println("$DOCKER run --rm=true \\");
             writer.println("\t--group-add keep-groups \\");
+            writer.println("\t--transient-store \\");
+
             if (_useLocalContainerStorage)
             {
                 getLogger().debug("Using local container storage: " + getLocalContainerDir().getPath());

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java
@@ -464,7 +464,7 @@ public Pair<File, File> downloadSra(String dataset, File outDir, boolean expectP
             List<String> args = new ArrayList<>();
             args.add(getExe().getPath());
 
-            args.add("-S");
+            // NOTE: we probably want the --split-3 behavior, which is the default for fasterq-dump
             args.add("--include-technical");
 
             Integer threads = SequencePipelineService.get().getMaxThreads(getLogger());