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WRROC fails with NullPointerException on initial run of nf-prov-test #40

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bentsherman opened this issue Feb 6, 2025 · 0 comments
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@bentsherman
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To reproduce, clone the nf-prov repository and run the test pipeline with nf-prov 1.4.0:

nextflow run nf-prov-test

It fails with the following error:

java.lang.NullPointerException: Cannot invoke "nextflow.processor.TaskRun.getWorkDir()" because "task" is null
	at nextflow.prov.WrrocRenderer.getTaskOutputName(WrrocRenderer.groovy:916)
	at nextflow.prov.WrrocRenderer.access$10(WrrocRenderer.groovy)
	at nextflow.prov.WrrocRenderer$_render_closure25.doCall(WrrocRenderer.groovy:459)
        ...
	at nextflow.prov.WrrocRenderer.render(WrrocRenderer.groovy:456)
	at nextflow.prov.ProvObserver.onFlowComplete(ProvObserver.groovy:123)
	at nextflow.Session.notifyFlowComplete(Session.groovy:1155)
	at nextflow.Session.shutdown0(Session.groovy:749)
	at nextflow.Session.destroy(Session.groovy:694)
	at nextflow.script.ScriptRunner.shutdown(ScriptRunner.groovy:260)
	at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:146)
	at nextflow.cli.CmdRun.run(CmdRun.groovy:376)
	at nextflow.cli.Launcher.run(Launcher.groovy:503)
	at nextflow.cli.Launcher.main(Launcher.groovy:658)

On a resumed run, the wrroc manifest is created successfully. So that is a workaround for now.

@fbartusch this looks like the same error you encountered with nf-core/demultiplex 1.5.1

Fortunately now that I'm seeing it with the test pipeline, it should be easy to debug and fix.

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