Direct execution of named (typed) workflows (module run)

[jorgee]

Draft. Ports PR #7208 ("Direct execution for named workflows"). Complements the workflow-modules PR (#7363) but is independent of it — this only touches the script/runtime layer, no module-system changes.

Enable running a single named, statically-typed workflow directly, without writing an explicit entry workflow. This is the execution primitive behind nextflow module run scope/name for workflow modules, and it also applies to a local nextflow run script.nf that defines exactly one named workflow.

What it does

Given a script with a single named, typed workflow:

nextflow.enable.types = true

workflow HELLO_SHEET {
    take:
    greetings: Channel<Map>   // samplesheet
    prefix: String            // scalar

    main:
    ...
    emit:
    result: Channel<String> = ...
}

nextflow run script.nf --greetings sheet.csv --prefix Hi

Nextflow synthesizes an entry workflow that maps --<take> params to the workflow inputs, invokes it, and publishes its emit: channels as outputs.

Changes

• nf-lang ScriptToGroovyVisitor — lower each workflow take with its declared type (_take_(name, type)) so take types are available at runtime.
• WorkflowDef / WorkflowParamsDsl — record take types and expose getDeclaredInputTypes(); untyped takes (Object) are omitted.
• ScriptMeta.hasExecutableWorkflows() — a non-module script with exactly one named workflow.
• BaseScript.run0() — when no entry is selected, synthesize an entry via WorkflowEntryHandler for a single named workflow, else fall back to the process entry handler; a multi-workflow script still reports "No entry workflow specified".
• WorkflowEntryHandler (new) — maps --<take> params to inputs using the declared types:
  • Channel<T> → load a samplesheet file (CSV / JSON / YAML) or wrap a collection with channel.fromList;
  • Value<T> → value channel;
  • scalar (String/Integer/Path/…) → coerced value.
    Then invokes the workflow and publishes its emits. Typed workflows only (guarded by isTypingEnabled()).

Not in this PR (follow-ups)

• Outputs reuse the existing OutputDsl publishing (as the process entry handler does); the ADR's no-output-directory / work-dir-path index-file behaviour is a follow-up.
• Typed-record samplesheets — rows currently load as Maps; casting each row to a custom record type (Channel<Sample>) is a follow-up (the __Params-class TODO from Direct execution for named workflows #7208).

Testing

• Unit: WorkflowEntryHandlerTest (samplesheet loading for CSV/JSON/YAML, param→take resolution by type, guards). Full nextflow.script.* and nf-lang suites pass.
• Manual e2e: ran a typed workflow with a Channel<Map> samplesheet take + a scalar String take via nextflow module run ./mod --greetings sheet.csv --prefix Hi → outputs published; verified the scalar is passed as a value and the CSV becomes a channel.

Co-authored from PR #7208 by @bentshermann.

[netlify]

✅ Deploy Preview for nextflow-docs canceled.

Name	Link
🔨 Latest commit	980e07c
🔍 Latest deploy log	https://app.netlify.com/projects/nextflow-docs/deploys/6a637e199b08e40008496f9d