new versions of toil seem to have a jobstore mandatory

dockstore · Nov 27, 2024 · 5deabba · 5deabba
1 parent 5122e51
commit 5deabba
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/dockstore-client/src/main/java/io/github/collaboratory/cwl/cwlrunner/ToilWrapper.java b/dockstore-client/src/main/java/io/github/collaboratory/cwl/cwlrunner/ToilWrapper.java
@@ -50,7 +50,7 @@ public List<String> getExecutionCommand(String outputDir, String tmpDir, String
         // than either physically available, or enforced by --maxDisk. Requested: 537944653824, Available: 134853001216" on trivial
         // workflows like md5sum
         ArrayList<String> command = new ArrayList<>(
-                Arrays.asList("toil-cwl-runner", "--logError", "--outdir", outputDir, "--tmpdir-prefix", tmpDir, "--tmp-outdir-prefix",
+                Arrays.asList("toil-cwl-runner", "--jobStore ./jobStore", "--logError", "--outdir", outputDir, "--tmpdir-prefix", tmpDir, "--tmp-outdir-prefix",
                         workingDir, cwlFile));
         jsonSettings.ifPresent(command::add);
         return command;