Fix module binaries on nextflow module run via session flag (#7087)

[pditommaso]

Summary

Fixes #7087 — alternative to #7088.

When a module is launched directly via nextflow module run <scope>/<name>, the module's main.nf is loaded as the entry script, not as an included module. As a result ScriptMeta.isModule() returns false for the script that owns the process, and TaskProcessor.getModuleBundle() returned null, so the resources/usr/bin directory was never injected into the task PATH -- even with nextflow.enable.moduleBinaries = true.

Approach

Track the "running as a module" state explicitly on the Session (run-scoped, not global), instead of widening the bundle gate:

• CmdRun exposes a protected boolean isModuleRun() hook (default false).
• CmdModuleRun overrides it to return true.
• CmdRun.run() propagates the value to the runner's session: runner.session.setModuleRun(isModuleRun()).
• TaskProcessor.getModuleBundle() now resolves the bundle when the owner script is either an included module (meta.isModule()) or the entry script of a module-run invocation (session.isModuleRun()).

// TaskProcessor.getModuleBundle()
if( meta?.scriptPath == null )
    return null
return (meta.isModule() || session.isModuleRun()) ? meta.getModuleBundle() : null

The feature remains opt-in via nextflow.enable.moduleBinaries.

How this differs from #7088

	#7088 (drop the gate)	This PR (session flag)
Change footprint	1 file, 1-line gate change	5 files: Session, CmdRun, CmdModuleRun, TaskProcessor, test
Gate semantics	Bundle resolved whenever the owner script has a known path	Bundle resolved only for included modules or module-run entry scripts
Behavior for plain nextflow run pipeline.nf with a sibling resources/	New: bundle picked up if moduleBinaries=true	Unchanged: bundle still ignored (exactly preserves previous behavior)
Risk of accidental bundle pickup	Low (still gated by feature flag), but the surface is broader	None: the new path is only reachable via nextflow module run
Plumbing	None	Adds Session.moduleRun + CmdRun.isModuleRun() hook

This variation is more conservative: it fixes the reported issue without changing what counts as a module-bundle source for any existing invocation other than nextflow module run. The trade-off is more plumbing (one new flag threaded from CLI to Session).

Possible side-effects and implications

• No effect when the feature flag is off. TaskProcessor.getBinDirs() still gates the call on session.enableModuleBinaries(), so default behavior is unchanged.
• No effect on nextflow run (with or without include). session.isModuleRun() is false for every CLI subcommand other than nextflow module run, so the gate behaves exactly as before for those invocations.
• No effect when there is no resources/ directory. ResourcesBundle.scan() returns an empty bundle when the directory does not exist, so getBinDirs() produces an empty list.
• Defensive guard added. A meta?.scriptPath == null early-return preserves robustness — ScriptMeta.getModuleBundle() would otherwise throw IllegalStateException if scriptPath were not yet set.
• API surface change. Session gains isModuleRun() / setModuleRun(boolean) and CmdRun gains a protected boolean isModuleRun() hook. These are minor additions but worth noting for downstream code that subclasses CmdRun.

Test plan

• ./gradlew :nextflow:test --tests "nextflow.processor.TaskProcessorTest" — new parameterized test should resolve module bundle for entry script when running as module … covers all three combinations:
  • included module (isModule=true, isModuleRun=false) → bundle resolved
  • module-run entry (isModule=false, isModuleRun=true) → bundle resolved (the fix)
  • plain entry (isModule=false, isModuleRun=false) → bundle NOT resolved (unchanged)
• ./gradlew :nextflow:test --tests "nextflow.SessionTest" --tests "nextflow.cli.CmdRunTest" passes.
• End-to-end repro from the issue (nextflow -c test.config module run cellgeni/failexample --greeting 'Hello world!') succeeds with this change applied — recommended manual verification before merge.

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[pditommaso]

Likely this is cleaner option vs #7088

[jorgee]

Changes look fine with me, just minor comments.
I wonder if, now that modules are in production, we could create a tests namespace and include integration tests, such as the one that is failing in this issue.

[jorgee]

Nit, there is an inconsistency with setters, setBinding and this one are using fluent but others like setBaseDir and setLibDir return void. Looking at the calls looks like it is not needed.