ProcessBuilder -> LabKeyProcessBuilder (#641)

* Migrate from ProcessBuilder to LabKeyProcessBuilder

* Migrate from ProcessBuilder to LabKeyProcessBuilder

Author: labkey-jeckels

nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java

@@ -29,6 +29,7 @@
 import org.labkey.api.security.SecurityManager;
 import org.labkey.api.targetedms.TargetedMSService;
 import org.labkey.api.util.FileType;
+import org.labkey.api.util.LabKeyProcessBuilder;
 import org.labkey.nextflow.NextFlowConfiguration;
 import org.labkey.nextflow.NextFlowManager;
 import org.labkey.vfs.FileLike;
@@ -88,12 +89,12 @@ public NextFlowRunTask(Factory factory, PipelineJob job)
             }
 
             // Need to pass to the main process directly in the future to allow concurrent execution for different users
-            ProcessBuilder secretsPB = new ProcessBuilder("nextflow", "secrets", "set", "PANORAMA_API_KEY", apiKey);
+            LabKeyProcessBuilder secretsPB = new LabKeyProcessBuilder("nextflow", "secrets", "set", "PANORAMA_API_KEY", apiKey);
             log.info("Setting secrets");
             FileLike dir = getJob().getLogFileLike().getParent();
             getJob().runSubProcess(secretsPB, dir);
 
-            ProcessBuilder executionPB = new ProcessBuilder(getArgs());
+            LabKeyProcessBuilder executionPB = new LabKeyProcessBuilder(getArgs());
             getJob().runSubProcess(executionPB, dir);
             log.info("Job Finished");
             NextFlowPipelineJob.LOG.info("Finished executing NextFlow: {}", getJob().getJsonJobInfo(true));