// 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.
Scaffold a complete Bactopia Tool across all three tiers -- module, subworkflow, and workflow entry point under workflows/bactopia-tools/. Creates all files (main.nf, module.config, schema.json, nextflow.config, tests) for the common single-tool pattern. Use when asked to add a new bactopia tool, create a bactopia tool, scaffold a complete tool, add a new analysis tool to bactopia-tools, or wire up a bioconda package as a bactopia-tool. This skill handles the full pipeline from package lookup through file generation -- do not use add-module or add-subworkflow separately when the goal is a complete bactopia-tool.
Scaffold a new Bactopia module from a bioconda/conda-forge package. Creates main.nf, module.config, schema.json, and test files following project standards. Use when asked to add a new module, create a new module, scaffold module files, or add a new tool's module.
Scaffold a new Bactopia subworkflow that orchestrates existing modules. Creates main.nf with GroovyDoc and test files. Use when asked to add a new subworkflow, create a subworkflow, or wire up modules into a subworkflow.
Show a live snapshot of the Bactopia project state — component counts, GroovyDoc coverage, nf-test coverage, and structural issues. Use when asked about project state, coverage, what's missing, what's documented, or what needs attention.
Review citation integrity across data/citations.yml and @citation tags using bactopia-citations --validate. Detects orphan citation keys (defined in the yml but never referenced) and workflow @citation keys that don't resolve to a yml entry. Use this skill whenever the user asks to review citations, check citation integrity, audit citations.yml, find orphan citations, clean up unused citations, validate workflow @citation tags, or verify that every tool cited in a workflow has a matching entry in the citations file.
Review staleness of reference docs under .claude/docs/ using bactopia-docs --validate. Detects deprecated patterns (residue from past migrations like flattenPaths, the 4-channel emission framing, meta:Map) and ground-truth violations (stale module/subworkflow/workflow counts, wrong Nextflow version, references to nonexistent bactopia-* commands or lint rule IDs, skill-inventory drift between 06-skills.md and .claude/skills/, broken markdown link targets). Use this skill whenever the user asks to review docs, check doc staleness, audit reference docs, find outdated documentation, verify doc claims, check if docs are current, or scan .claude/docs for drift after a migration.
| name | merge-schemas |
| description | 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. |
Regenerate the nextflow.config and nextflow_schema.json files for one or more Bactopia workflows by invoking bactopia-merge-schemas. Auto-discovers each workflow's output directory from catalog.json so the caller never hand-computes paths.
Identify the target workflow(s). Parse the user's request into one of these shapes:
teton, merlin, bactopia)teton and staphopia) or a glob-ish pattern (e.g. all merlin tools, everything starting with blast)all tools → every workflow with type: tool in the catalogall named → every workflow with type: namedall → every workflow in the catalogIf the ask is ambiguous (e.g. "regenerate merlin" — merlin is a named Bactopia Tool entry but also a subworkflow tag), confirm with the user before running anything. Never run without some kind of filter.
Resolve each target to a path from the catalog. Use the Read tool to read /home/rpetit3/repos/bactopia/bactopia/catalog.json. For each requested workflow W:
catalog["workflows"][W] exists. If not, stop and report the unknown name — do not invoke the CLI.catalog["workflows"][W]["path"] — this is the exact value to pass as --outdir. It is already relative to the repo root:
. → main bactopia workflow (outputs land in the repo root)workflows/teton/ / workflows/staphopia/ / workflows/cleanyerreads/ → named workflowsworkflows/bactopia-tools/{name}/ → Bactopia Toolscatalog["workflows"][W]["type"] (named vs tool) for the summary.Check for existing generated files. For each target --outdir, use Read or Glob to check whether nextflow_schema.json or nextflow.config already exist. If any do:
--force--force, the CLI exits with an error on the first existing fileDo not pass --force preemptively — it is a destructive overwrite of tracked files.
Run bactopia-merge-schemas once per target via the wrapper:
bash .claude/skills/merge-schemas/scripts/run-bactopia-merge-schemas.sh \
--bactopia-path /home/rpetit3/repos/bactopia/bactopia \
--wf <workflow> \
--outdir <path-from-catalog> \
--force # only if the user confirmed in step 3
Run sequentially. On the first failure, stop and report — do not silently continue through a batch.
Summarize the result. For each target, report:
named / tool)--outdir usednextflow_schema.json, nextflow.config)If nothing was regenerated (e.g. all targets refused --force), say so explicitly.
bactopia-merge-schemas (PATH → bactopia-dev conda env → bactopia-py conda env → any bactopia-* env)--bactopia-path is always /home/rpetit3/repos/bactopia/bactopia — do not guess or prompt--outdir always comes from catalog["workflows"][wf]["path"] — never hand-compute itnextflow_schema.json and nextflow.config. The source also declares params.config / process.config variables and includes them in its pre-flight existence check, but does not actually write them. If the user expects those files, tell them the current CLI does not generate them--force is required if either of the two output files already exists. Ask firstconf/schema/{wf}.json backs named workflows; conf/schema/bactopia-tools.json backs tools. Generic parameters come from conf/schema/generic.json. You do not need to touch these files — the CLI reads them directlybactopia, teton, staphopia, cleanyerreads) and ~66 tools under workflows/bactopia-tools/bactopia-merge-schemas)Required:
--bactopia-path PATH — repo root--wf NAME — workflow key from catalog.jsonOutput:
--outdir PATH — directory to write outputs (default .)--force — overwrite existing output filesOther:
--verbose / --silent — log level--version / --help/update-module — bumps tool versions in module.config and CHANGELOG.md. When a module update changes that module's schema.json, /merge-schemas is the right follow-up for every workflow that includes the module./project-status — shows coverage and structural issues; useful for confirming catalog state before batch regeneration.