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nf-core-module-dev
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.
What's Inside
Agents3
nf-module-dev
/nf-module-dev
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: ..."
nf-secretary
/nf-secretary
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"
nf-test-expert
/nf-test-expert
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"
Skills2
nf-module-manager
/nf-module-manager
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"
using-nf-core-module-dev
/using-nf-core-module-dev
Loaded at session start — establishes when to use nf-core module dev agents and skills
Stats
Version1.3.0
Released
LanguageShell
Stars8
MaintenanceExcellent
LicenseMIT
Last Commit
Added
Available In
Safety Signals
Caution
Uses power tools
Uses Bash, Write, or Edit tools
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