From 13613bd7d6611ba7399dc6d21201b4efc92aef7d Mon Sep 17 00:00:00 2001 From: labkey-jeckels Date: Fri, 29 May 2026 13:22:48 -0700 Subject: [PATCH 1/2] Migrate from ProcessBuilder to LabKeyProcessBuilder --- nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java index 8e996b6c..b9b4e6cc 100644 --- a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java +++ b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java @@ -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; @@ -73,7 +74,7 @@ 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); From 2d1071c0d18000cc97f3ea13067f0007c510e42b Mon Sep 17 00:00:00 2001 From: labkey-jeckels Date: Fri, 29 May 2026 13:45:12 -0700 Subject: [PATCH 2/2] Migrate from ProcessBuilder to LabKeyProcessBuilder --- nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java index b9b4e6cc..48429856 100644 --- a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java +++ b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java @@ -79,7 +79,7 @@ public NextFlowRunTask(Factory factory, PipelineJob job) 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));