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Port remaining changes from nextflow-io/agent-skills - #10
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- Add workflow module support to run-module, registry composition and install-nextflow (nextflow-io/agent-skills#14) - Replace migrate-nextflow-code with the upstream version, which relies on the Nextflow docs and `nextflow lint` type checking instead of bundled references and language server scripts (nextflow-io/agent-skills#15) - Drop the agent-skills upstream from sources.json, since that repo is being archived in favor of this one - Document installing the skills without the plugin via `npx skills` and `gh skill`
Carry over the still-relevant guidance from nextflow-io/agent-skills, plus the sources.json hash and release steps for this repo.
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Now that I'm thinking about it, should we move maintain NF core pipeline to the NF core agents repo? https://github.com/nf-core/agents
| 2. **Look for workflow modules** that already cover a chain of steps. `nextflow module search` rarely ranks them high enough to appear, so query the registry API with the `kind=Workflow` filter: | ||
| ```bash | ||
| curl -s "https://registry.nextflow.io/api/v1/modules?query=align%20reads%20STAR&kind=Workflow&limit=10" \ | ||
| | python3 -c 'import json,sys; [print(r["name"], "-", r["description"]) for r in json.load(sys.stdin)["results"]]' | ||
| ``` |
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Could we fix this at the registry level then?
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That's a Paolo-ism, he insisted on not including workflows by default in the search 🤷
For now I'm just porting the current state from nextflow-io. Feel free to make a follow-up PR
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We need to add the LSP as part of the plugin, claude code supports it out of the box
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I tried this but the claude <-> LSP integration is no good for nextflow. When the LSP returns diagnostics across multiple files it only shows the base file name, so claude sees main.nf for every file and can't tell which file is which
This PR ports the changes made in nextflow-io/agent-skills since it was imported here (at
1edf737), so that the agent-skills repo can be archived in favor of this one.Changes
Workflow modules (nextflow-io/agent-skills#14)
run-module: explain process vs workflow modules, find workflow modules via the registry APIkind=Workflowfilter, and handle untyped workflow modules ("cannot be executed directly because it is not typed")build-nextflow-pipelineregistry composition: look for workflow modules when planning, defer untyped workflow modules to the end-to-end run, and document how to include and call theminstall-nextflow: note that workflow modules require Nextflow 26.10+migrate-nextflow-code (nextflow-io/agent-skills#15)
SKILL.md, links to the Nextflow docs instead of bundling hard-coded examples, and usesnextflow lint(which type checks as of 26.10) instead of the language server scriptsscripts/nextflow-typecheck.shandscripts/nextflow-language-server.shdisable-model-invocationrepair-workflow,maintain-nf-core-pipelineand the README to themigrate-nextflow-codeskilltools/skill_consolidations.jsonProvenance
github_upstreamsinsources.json, along with its per-file entries and entries for deleted files. Recompute hashes for the files edited above.NOTICEand the license copy are kept for attributionREADME
npx skills add seqeralabs/nextflow-pluginandgh skill install seqeralabs/nextflow-pluginAGENTS.md
sources.jsonhash rule for this repoTesting
python3 -I tools/check_sources.py: 114 files, 0 errorspython3 -I tools/test_consolidate_skills.py: 7 tests OKclaude plugin validate --strict .: passednpx skills add seqeralabs/nextflow-plugin --listdiscovers the skillsThe plugin version is not bumped.