Scaffolds a complete Bactopia Tool pipeline from a bioconda package.
npx skills add https://github.com/bactopia/bactopia --skill add-bactopia-tool
Please help me install this Agent Skill. Skill: add-bactopia-tool Source: https://github.com/bactopia/bactopia/tree/main/.claude/skills/add-bactopia-tool Command: npx skills add https://github.com/bactopia/bactopia --skill add-bactopia-tool
Scaffold a complete Bactopia Tool across all three tiers—module, subworkflow, and workflow entry—under workflows/bactopia-tools/. It creates all necessary files (main.nf, module.config, schema.json, nextflow.config, tests) so you can add a bactopia tool with minimal manual setup.
Ask the tool to scaffold a new bactopia-tool from a bioconda package and it will generate all three tiers ready for customization.
High-intent search queries and answers about installing and using this skill.
Scaffolding a Nextflow tool from a bioconda package generates a complete three-tier Bactopia pipeline structure, creating modules, subworkflows, and workflow entry points with minimal manual setup.
When adding a bactopia tool, you typically need main.nf, module.config, schema.json, nextflow.config, and tests. This Skill automates that by generating all necessary scaffolding files across the module, subworkflow, and workflow tiers automatically.
Yes, wiring a conda package into bactopia-tools does not require writing Nextflow code from scratch because the Skill performs package lookup and generates the required module, subworkflow, and workflow scaffolds ready for customization.
Yes, this scaffolding workflow supports both bioconda and conda-forge packages by looking up the specified package and scaffolding the common single-tool pattern across the complete Bactopia tool pipeline tiers.
The three-tier structure in Bactopia tool development organizes pipelines into module, subworkflow, and workflow entry tiers, allowing you to scaffold a complete tool pipeline from a single bioconda package and customize each level independently.
bactopiaScaffold Bactopia modules from Bioconda packages with standard files and tests.
bactopiaScaffold Bactopia subworkflows with main.nf, tests, and configuration files.
bactopiaRegenerate nextflow.config and nextflow_schema.json for Bactopia workflows.
sensei-hackerCheck GitHub Actions CI build status for pull requests and workflow runs.
