Derive the nextflow branch key and URL from the workflow being run - #14
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jbrestel wants to merge 1 commit into
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Derive the nextflow branch key and URL from the workflow being run#14jbrestel wants to merge 1 commit into
jbrestel wants to merge 1 commit into
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runAndMonitor read the nextflowWorkflow param to build the "<workflow>.branch" shared config key, which is only correct while a step runs exactly one workflow. Take both the branch key and the github URL from the workflow name it is handed so a step class can run more than one workflow, and pass the bare name in. No change for existing callers: they hand it the same workflow the param holds. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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Why
runAndMonitorbuilt the<workflow>.branchshared-config key by re-reading the step'snextflowWorkflowparam:That is only correct while a step runs exactly one workflow.
ApiCommonWorkflowis merging its ngs-samples fetch and its analysis run into a single step (VEuPathDB/ApiCommonWorkflow#101) so the pair holds one throttle slot; without this change the ngs-samples run would pick up the analysis workflow's branch config.What
runAndMonitornow takes the bare workflow name and derives both the branch key and thehttps://github.com/…URL from it.runpasses the name through instead of pre-building the URL.Risk
None for existing callers — every one hands
runAndMonitorthe same workflow itsnextflowWorkflowparam holds, so the key and URL are unchanged.runis otherwise untouched, which matters becauseMicrobiomeWorkflowuses this class directly (runHumannOnCluster.xml,runEukdetectOnCluster.xml).The only subclass in the org,
ApiCommonWorkflow::…::RunAndMonitorNextflowNGSSamples, is deleted by the companion PR.RunAndMonitorNextflowWithEntryis an independent copy-paste fork of this class and is unaffected.Testing
StepClasses/t/run_and_monitor_nextflow.t: 2 pass, 1 fails —tailLooksOk"Retried but failed" expects''and getsundef. Confirmed pre-existing: it fails identically with this change stashed.Behaviour is covered end-to-end by the companion PR's
Main/t/run_ngs_samples_and_nextflow.t(21 assertions).Merge order
Merge this first, or together with VEuPathDB/ApiCommonWorkflow#101 — that PR's new step class depends on it.
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