Add nextflow module generate-meta command

[jorgee]

Summary

• Adds nextflow module generate-meta CLI subcommand that parses a module's main.nf and generates a meta.yml template pre-populated with all inferable values
• Supports both V1 (classic qualifier syntax: val, path, tuple) and V2 (static type syntax: reads: Path, (meta, reads): Tuple<String, Path>)
• Implements two-pass static analysis for V2 output type inference: builds a symbol map from input parameters and exec block assignments, then resolves output types via declared type → symbol map lookup → RHS expression inference chain
• Adds -force flag to overwrite an existing meta.yml and -dry-run flag to print to stdout without writing

Changes

• CmdModule.groovy — registers the new generate-meta subcommand
• ModuleGenerateMeta.groovy — CLI entry point with path resolution, overwrite guard, dry-run routing
• MetaYmlGenerator.groovy — AST extraction (V1 + V2) and YAML rendering via SnakeYAML
• MetaYmlGeneratorTest.groovy — 14 Spock unit tests covering V1 qualifiers, V2 typed inputs, symbol map inference, tuple sub-entries, YAML rendering
• ModuleGenerateMetaTest.groovy — 10 Spock CLI tests covering generation, overwrite guard, dry-run, error cases
• VariableScopeVisitor.java — minor related fix

Test plan

• Run ./gradlew :nextflow:test --tests "nextflow.module.MetaYmlGeneratorTest" — all 14 tests pass
• Run ./gradlew :nextflow:test --tests "nextflow.cli.module.ModuleGenerateMetaTest" — CLI tests pass
• Manual: nextflow module generate-meta <module-dir> generates a valid meta.yml
• Manual: re-running without -force errors; with -force regenerates; -dry-run prints to stdout

🤖 Generated with Claude Code

[jorgee]

Update:

• Rename generate-meta subcommand by spec
• Allow module reference as primary argument and add -scope when fullname is not possible
• Remove TODOS in module fields. Still in input/output descriptions or when no type could be inferred.
• Input/Output validation in ModuleSpec to avoid pushing arguments with TODOs
• Some refactor: ModuleGenerataMeta renamed to CmdModuleSpec and MetaYmlGenerator integrated in ModuleSpec

[pditommaso]

Nit, I'd likely call this create-meta there's a more canonical term for file creation (I understand that now "generate" feels trendy ..)

[pditommaso]

Code Review Findings

Critical (Must Fix)

1. Bug: authors guarded by license check in asMap()
ModuleSpec.groovy:293-294 — checks this.license instead of this.authors:

// CURRENT (wrong)
if( this.license )
    manifest['authors'] = this.authors

// FIX
if( this.authors )
    manifest['authors'] = this.authors

Authors will be silently dropped when license is null, or emit null when license is set but authors isn't.

2. Potential NPE in extractMethodCallType
ModuleSpec.groovy:776 — methodTarget can be null for unresolved method calls:

// CURRENT (missing null-safe on methodTarget)
return resolveTypeFromDeclaredType(simpleTypeName(methodExpr.methodTarget.returnType?.name))

// FIX
return resolveTypeFromDeclaredType(simpleTypeName(methodExpr.methodTarget?.returnType?.name))

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Important (Should Fix)

#	Issue	Location
3	YAML header still says generate-meta instead of spec	ModuleSpec.groovy:58
4	moduleName field lacks type declaration in @CompileStatic class	CmdModuleSpec.groovy:71
5	validate() checks type.equals(DESCRIPTION_TODO) — should be description.equals(DESCRIPTION_TODO)	ModuleSpec.groovy:87
6	resolveAsPath uses args[0] instead of module param	CmdModuleSpec.groovy:129

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Suggestions

• buildParamSpec always emits DESCRIPTION_TODO even if entry.description is already populated (line 323)
• load() doesn't close the InputStream from Files.newInputStream (line 141)
• Log messages reference $args (full list) instead of $module (lines 117, 119, 123)
• No test covering the authors field rendering in asMap() — would have caught bug A process that define only an input of type 'each' never stops #1

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🤖 Generated with Claude Code

[jorgee]

Nit, I'd likely call this create-meta there's a more canonical term for file creation (I understand that now "generate" feels trendy ..)

@ben suggested to call it 'spec'. This is the name in the current implementation. 'create-meta', 'create-spec' are also good alternatives to me.

I fixed other issues and comments. Apart from the name, it is ready for review from my side

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