Support workflow modules (kind: Workflow) in the module system

[jorgee]

Draft — stacked on #7342 (the workflow-modules ADR). Base is adr-workflow-modules so the diff shows only the implementation; retarget to master once #7342 lands.

Implements the workflow modules feature from the ADR (#7342): the module system is extended to support standalone workflow modules (kind: Workflow) alongside process modules — published, installed, resolved, included, and (via a follow-up PR) executed through the existing registry / nextflow module CLI infrastructure.

What's implemented

Spec model & schema

• ModuleSpec/ModuleSpecFactory parse a top-level kind (Process|Workflow, default Process) and a nested requires.modules list of direct dependencies.
• adr/module-spec-schema.json allows kind, requires.modules (exact-pin references), nested scope/name names, and adds channel / custom-record to the parameter type enum as documentation tags for statically-typed declarations.

Install / include

• Nested vendoring — ModuleResolver installs a workflow module together with its transitive dependencies, each vendored under its own nested modules/ directory (modules/<scope>/<name>/modules/...). No cross-module flattening — duplication accepted per the ADR's diamond-dependency decision — plus dependency-cycle detection.
• Context-relative include resolution — the runtime path (IncludeDef) and both compile-time paths (nf-lang ResolveIncludeVisitor and the source-discovery ModuleResolver) resolve a module's remote includes relative to the including file's directory, so a workflow module's own includes find its nested dependencies.
• Integrity checksum covers the module's full installed subtree (own files + vendored deps), computed after vendoring — so a freshly installed workflow-with-deps reads VALID, and edits to either the module or a vendored dependency are detected as MODIFIED.
• module install -update-deps — for an already-installed module, re-vendors its dependencies to match the (possibly locally-edited) meta.yml without reinstalling the module itself: installs new deps, updates changed versions, prunes removed ones (a locally-modified dependency is never silently overwritten or pruned). Ignored when the module is not installed; mutually exclusive with -force.

Publish / validate

• kind-aware validation: a workflow module must define exactly one workflow; when its meta.yml declares input/output, the counts must match the workflow's take:/emit: arity.
• requires.modules are validated against the registry at publish time (they exist at their pinned version), since dependencies are re-resolved from the registry by consumers at install time.
• Nested vendored dependencies are excluded from the publish bundle (consumers re-resolve them from the registry).
• Schema-location override (-schema flag, NXF_MODULE_SPEC_SCHEMA env, or meta.yml $schema).

nextflow module CLI — kind awareness

• list — shows a Kind column (and kind JSON field).
• create — -kind Process|Workflow and -typed. Typed scaffolds set nextflow.enable.types and use typed input/output (process) or take/emit (workflow); the generated meta.yml follows suit, and typed process/workflow declare the minimum Nextflow version that introduced them (25.10.0 / 26.04.0). An untyped workflow scaffold documents its channel take/emit.
• spec — supports workflow modules, deriving input/output from the workflow's take:/emit: (types inferred when statically typed; TODO placeholder otherwise).
• search / view — show the module kind (formatted + JSON), defaulting to Process.

Registry dependency (npr-api 0.24.10 → seqeralabs/nextflow-registry#366)

The kind shown by module search / module view comes from the registry API, which added kind to ModuleSearchResult / ModuleMetadata in seqeralabs/nextflow-registry#366 (npr-api 0.24.10). This branch bumps io.seqera:npr-api / npr-client to 0.24.10.

CI will not pass until npr-api 0.24.10 is published to the Seqera Maven repository. To build and test locally in the meantime:

# 1. Build the registry API client from PR #366 (VERSION 0.24.10) and publish it to local Maven
cd <nextflow-registry checkout on seqeralabs/nextflow-registry#366>
./gradlew :npr-api:publishToMavenLocal :npr-client:publishToMavenLocal

# 2. In this repo, add mavenLocal() to the repositories block in build.gradle (do NOT commit this):
#    repositories {
#        mavenLocal()
#        mavenCentral()
#        ...
#    }

# 3. Build / run nextflow as usual
make compile

Not in this PR (follow-ups)

• Direct typed execution nextflow module run scope/name — entry-workflow synthesis from take:/emit:, samplesheet input loading, and work-dir-path outputs — is in a separate PR.
• module search --kind filter (registry-side support needed).
• Typed-record samplesheet loading and the ADR's no-output-directory / index-file outputs (both follow-ups of the module-run PR).

Testing

• Unit: ModuleSpecFactoryTest (process + workflow spec, typed types, channel/custom-record), ModuleValidatorTest, ModuleSchemaValidatorTest, ModuleResolverDependencyTest (nested install layout, per-consumer duplication, cycle detection, auto-install, checksum/integrity, -update-deps), ModuleStorageTest (bundle excludes nested modules/), CmdModuleCreateTest, CmdModuleListTest, CmdModulePublishTest, CmdModuleSearchTest, CmdModuleViewTest.
• Manual e2e: published a kind: Workflow module (adapted from nf-core mafft_align + its mafft/align dependency) to a dev registry, ran module install, and included/composed it in a pipeline — verified working.

Notes

• The registry-side changes (persisting/serving kind + requires.modules, exposing kind on search/view) are in seqeralabs/nextflow-registry#366.