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ProcessBuilder -> LabKeyProcessBuilder #641

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ProcessBuilder -> LabKeyProcessBuilder #641

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13613bd
Migrate from ProcessBuilder to LabKeyProcessBuilder
labkey-jeckels May 29, 2026
2d1071c
Migrate from ProcessBuilder to LabKeyProcessBuilder
labkey-jeckels May 29, 2026
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5 changes: 3 additions & 2 deletions nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
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;
Expand Down Expand Up @@ -73,12 +74,12 @@ 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));
Expand Down