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merge-schemas

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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.

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How to use this skill

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Source SKILL.md: https://github.com/bactopia/bactopia/blob/HEAD/.claude/skills/merge-schemas/SKILL.md

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Merge Schemas

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.

Steps

  1. Identify the target workflow(s). Parse the user's request into one of these shapes:

    • A specific workflow name (e.g. teton, merlin, bactopia)
    • A list (e.g. 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 catalog
    • all named → every workflow with type: named
    • all → every workflow in the catalog

    If 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.

  2. 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:

    • Verify catalog["workflows"][W] exists. If not, stop and report the unknown name — do not invoke the CLI.
    • Pull 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 workflows
      • workflows/bactopia-tools/{name}/ → Bactopia Tools
    • Record catalog["workflows"][W]["type"] (named vs tool) for the summary.

  3. 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:

    • List the affected workflows and files for the user
    • Get explicit confirmation before proceeding with --force
    • Without --force, the CLI exits with an error on the first existing file

    Do not pass --force preemptively — it is a destructive overwrite of tracked files.

  4. 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.

  5. Summarize the result. For each target, report:

    • Workflow name and type (named / tool)
    • The --outdir used
    • Which files were generated (nextflow_schema.json, nextflow.config)
    • Pass/fail status

    If nothing was regenerated (e.g. all targets refused --force), say so explicitly.

Notes

  • The wrapper auto-discovers 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 it
  • The CLI writes only two files: nextflow_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 first
  • conf/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 directly
  • Typical catalog contents: 4 named workflows (bactopia, teton, staphopia, cleanyerreads) and ~66 tools under workflows/bactopia-tools/

CLI Reference (bactopia-merge-schemas)

Required:

  • --bactopia-path PATH — repo root
  • --wf NAME — workflow key from catalog.json

Output:

  • --outdir PATH — directory to write outputs (default .)
  • --force — overwrite existing output files

Other:

  • --verbose / --silent — log level
  • --version / --help

Sibling Skills

  • /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.