Regenerate nextflow.config and nextflow_schema.json for Bactopia workflows.
npx skills add https://github.com/bactopia/bactopia --skill merge-schemas
Please help me install this Agent Skill. Skill: merge-schemas Source: https://github.com/bactopia/bactopia/tree/main/.claude/skills/merge-schemas Command: npx skills add https://github.com/bactopia/bactopia --skill merge-schemas
Regenerate nextflow.config and nextflow_schema.json for Bactopia workflows by running bactopia-merge-schemas. Use when asked to merge schemas, regenerate workflow config, rebuild nextflow_schema.json, or sync workflow configs after module schema changes.
Run bactopia-merge-schemas to regenerate schema and config files for the target workflows.
High-intent search queries and answers about installing and using this skill.
To regenerate nextflow_schema.json for Bactopia workflows, run bactopia-merge-schemas to sync workflow configurations. This operation targets workflows via catalog.json and automatically rebuilds both the schema and nextflow.config files.
The best way to sync nextflow.config files is by running bactopia-merge-schemas to regenerate schemas for multiple workflows. You can target workflows broadly using categories like all tools, all named, or all workflows discovered via catalog.json.
Yes, you can target specific Bactopia workflows for schema regeneration using exact names, lists, or glob patterns. The tool resolves these targets via catalog.json to precise output directories and determines the workflow type for accurate reporting.
Yes, you need conda and python3 installed in your environment to rebuild nextflow schemas. The schema regeneration process relies on a wrapper to locate and execute bactopia-merge-schemas, which requires these dependencies to function correctly.
Bactopia-merge-schemas checks for existing output files before regenerating workflow configs to validate current states and prevent unnecessary overwrites. This validation step ensures the merge-schemas operation only processes targets requiring updates, summarizing results with per-target status.
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