feat: Implement Wave CLI as Nextflow first-class command#98
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edmundmiller wants to merge 3 commits intoseqeralabs:masterfrom
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feat: Implement Wave CLI as Nextflow first-class command#98edmundmiller wants to merge 3 commits intoseqeralabs:masterfrom
edmundmiller wants to merge 3 commits intoseqeralabs:masterfrom
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Transform standalone Wave CLI into wave-cli Nextflow plugin architecture. Implement PluginAbstractExec interface, migrate to modern plugin structure, and preserve all existing CLI functionality. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
- Add WaveCommand extending CmdBase for full CLI integration - Add WaveCommandExtensionPoint to register 'wave' as first-class command - Integrate with existing Wave CLI application seamlessly - Support all Wave CLI features including help, options, and examples Users can now execute 'nextflow wave' directly instead of verbose 'nextflow plugin nf-wave:command' syntax. The command appears in main Nextflow help output with description and full functionality. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
- Update build.gradle with nextflow-plugin gradle plugin and dependencies - Configure settings.gradle for plugin development workflow - Update Makefile for streamlined build and installation process - Configure WavePlugin main class for proper extension registration - Update extensions.idx to register WaveCommandExtensionPoint Enables independent development and distribution of Wave CLI as a standalone Nextflow plugin while maintaining full integration with the main Nextflow CLI system. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
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Summary
This PR enables Wave CLI to work as a first-class Nextflow command:
nextflow waveinstead ofnextflow plugin nf-wave:command.Changes
WaveCommand.groovy- integrates with Nextflow CLI systemWaveCommandExtensionPoint.groovy- registers the wave commandUsage
The wave command now appears in main Nextflow help output alongside built-in commands.
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