By vagkaratzas
Create, test, and document Nextflow nf-core modules end-to-end: generate main.nf and environment.yml, write and fix nf-test files, and produce or update meta.yml to pass nf-core linting.
Use this agent when a module's main.nf or environment.yml needs to be created or updated. This includes creating a brand new nf-core module from scratch, or updating an existing module's main.nf (e.g. new inputs/outputs, script changes) and environment.yml (e.g. new bioconda package version). Does NOT write tests or meta.yml — those are handled by nf-test-expert and nf-secretary. Examples: - User: "Create an nf-core module for bwa mem2 mem" - User: "Update the samtools/sort module to support a new optional input" - User: "A new version of fastp is on bioconda, update the module" - nf-module-manager: "Create the scaffold and main.nf for gemmi/cif2json" - nf-module-manager: "Fix the output channel names in apbs/main.nf per these errors: ..."
Use this agent when the user needs to update, create, or fix meta.yml files for nf-core Nextflow modules or subworkflows. This includes when a new module/subworkflow is created, when main.nf inputs/outputs change, or when meta.yml files need to conform to the nf-core schema and pass linting. Examples: - user: "Update the meta.yml for samtools/sort" - user: "I changed the inputs in my fastqc module's main.nf" - user: "nf-core modules lint is failing on my module's meta.yml" - user: "Document this new subworkflow I created"
Use this agent when the user asks to write, create, generate, or fix an nf-test for a Nextflow or nf-core module, subworkflow, or pipeline. Also use when asked to generate or update test snapshots, debug failing nf-tests, or review nf-test files. Examples: - User: "Write an nf-test for the new fastqc module" - User: "Create tests for my subworkflow in modules/subworkflows/nf-core/mysubworkflow" - User: "The snapshot for my pipeline test is failing, can you fix it?" - User: "Generate nf-tests for the proteinfamilies pipeline"
Use this skill when the user wants a complete nf-core module built end-to-end: scaffolded, tested, and documented. Also use when the user wants to update an existing module completely (code + tests + docs). Examples: - User: "Create an nf-core module for samtools sort" - User: "I need a full nf-core module for bwa mem with tests and docs" - User: "Set up the nf-core module structure for trimmomatic trimpe" - User: "Update the apbs module end-to-end"
Loaded at session start — establishes when to use nf-core module dev agents and skills
Uses power tools
Uses Bash, Write, or Edit tools
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A Claude Code plugin that gives your coding agent specialised skills for creating, testing, and documenting nf-core Nextflow modules.
When you ask Claude to build an nf-core module, it doesn't just start writing code. The nf-module-manager skill orchestrates a structured pipeline:
main.nf and environment.yml to nf-module-dev, which researches the tool, scaffolds the module, and populates it following current nf-core conventions.meta.yml.Each agent is a specialist:
| Agent | Responsibility |
|---|---|
nf-module-dev | main.nf, environment.yml |
nf-test-expert | nf-tests, snapshots |
nf-secretary | meta.yml, linting |
Because the nf-module-manager runs as a skill in your main session (not a hidden sub-agent), you can watch every step as it happens.
claude plugin marketplace add vagkaratzas/nf-core-module-dev
claude plugin install nf-core-module-dev@vagkaratzas
Then start a new session. The plugin bootstraps automatically — you get the full experience: the three specialists plus the nf-module-manager orchestrator.
Codex can use the same marketplace repository. Add the marketplace, then install the plugin from the Codex plugin browser:
codex plugin marketplace add vagkaratzas/nf-core-module-dev
codex
# In Codex: /plugins
# Select the vagkaratzas marketplace, then install nf-core-module-dev.
claude plugin marketplace update vagkaratzas
claude plugin update nf-core-module-dev@vagkaratzas
Then restart Claude Code.
If the configured marketplace or plugin name differs:
claude plugin marketplace list
claude plugin list
codex plugin marketplace upgrade vagkaratzas
Then restart Codex and reinstall nf-core-module-dev from /plugins.
For a complete end-to-end module build, just describe what you want:
"Create an nf-core module for
bwa-mem2 mem"
Claude will invoke the nf-module-manager skill and orchestrate the full pipeline.
For targeted work, agents can be invoked directly:
"Write an nf-test for the
clipkitmodule"
"Fix the meta.yml lint errors insamtools/sort"
"Updateeggnogmapperto the latest bioconda version"
main.nf and environment.yml following current nf-core style. Stops and waits for you if a bioconda/container environment can't be auto-detected.meta.yml, handles topic-based versions, EDAM ontologies, and all known schema edge casesnf-core CLI installed and on your PATHnf-test installed and on your PATHAgents carry their domain knowledge as embedded reference sections — no separate memory files. To contribute a fix or new pattern:
## Reference: ... section in the agent .md fileVersion numbers are kept in sync across the Claude marketplace, Claude plugin manifest, and Codex plugin manifest using the included bump script:
# Check versions are in sync
scripts/bump-version.sh --check
# Bump to a new version
scripts/bump-version.sh 1.1.0
MIT
npx claudepluginhub vagkaratzas/nf-core-module-dev --plugin nf-core-module-devComplete collection of battle-tested Claude Code configs from an Anthropic hackathon winner - agents, skills, hooks, and rules evolved over 10+ months of intensive daily use
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