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Agent skill

Merge Schemas

by bactopia in bactopia/bactopia

Regenerate nextflow.config and nextflowschema.json for Bactopia workflows by running bactopia-merge-schemas.

MITAuto-check passedResearch & Science

Install Merge Schemas

skills CLI
$ npx skills add bactopia/bactopia --skill merge-schemas -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install bactopia/bactopia merge-schemas --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/bactopia/bactopia.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.agents/skills/merge-schemas .claude/skills/merge-schemas && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
merge-schemas
GitHub stars
522
Token cost
~1.3k tokens
SKILL.md length
565 words
Files
2 (incl. scripts)
Skills in repo
15
Repo updated
First seen
Licence
MIT

At a glance

Regenerate nextflow.config and nextflowschema.json for Bactopia workflows by running bactopia-merge-schemas.

  • Works in 5 steps: Identify the target workflow(s). Parse… → Resolve each target to a path from the… → Check for existing generated files. For… → …
  • Asked to merge schemas
  • SKILL.md covers Steps and Notes
  • Runs Shell scripts from its folder

What it does

Merge Schemas is an agent skill from bactopia/bactopia. Regenerate nextflow.config and nextflowschema.json for Bactopia workflows by running bactopia-merge-schemas. Use when asked to merge schemas, regenerate workflow config, rebuild nextflowschema.json, or sync workflow configs after module schema changes.

Its SKILL.md is about 1.3k tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files, including scripts (for example `scripts/run-bactopia-merge-schemas.sh`).

It sits in Research & Science, covering Reproducible research. It works with Nextflow. The repository describes itself as: A flexible pipeline for complete analysis of bacterial genomes. The licence is MIT.

When your agent uses it

  • Asked to merge schemas
  • Regenerate workflow config
  • Rebuild nextflowschema.json
  • Sync workflow configs after module schema changes

Example prompts

  • “/merge-schemas”

Requirements

  • A Bash shell

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

  1. Identify the target workflow(s). Parse the user's request into one of these shapes
  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…
  3. Check for existing generated files. For each target --outdir, use Read or Glob to check whether nextflow_schema.json or nextflow.config…
  4. Run bactopia-merge-schemas once per target via the wrapper
  5. Summarize the result. For each target, report

What it can do on your machine

Read from SKILL.md and the folder at commit 29fb741. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 1 file in scripts/ (Shell), which the agent can run.

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Merge Schemas loads about 1.3k tokens when it runs. Until then it costs about 67 tokens; SKILL.md has 565 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~67
When it runs · the whole SKILL.md, loaded when a task matches
~1.3k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from bactopia/bactopia at commit 29fb741, republished under its MIT licence (© bactopia). 565 words, ~1,254 tokens.

Download SKILL.mdSave it as .claude/skills/merge-schemas/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.
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.

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 .agents/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.

Show full SKILL.md (209 more words)Show less

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.

© bactopia, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 1 other file (scripts) in .agents/skills/merge-schemas of bactopia/bactopia.

  • SKILL.md
  • scripts/run-bactopia-merge-schemas.sh

Open the folder on GitHubat commit 29fb741

Compare with similar skills

Merge Schemas next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Merge Schemas compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Merge Schemas this skillbactopia/bactopia522—~1.3kAutomated safety check: PassMIT
LaminDB Biological Data Managementdavila7/claude-code-templates32k12 repos~3.6kAutomated safety check: PassMIT
Latchbio Integrationdavila7/claude-code-templates32k11 repos~2.4kAutomated safety check: PassMIT
PacsomaticBioTender-max/awesome-bio-agent-skills199—~1.3kAutomated safety check: PassMIT
Latchbio IntegrationK-Dense-AI/scientific-agent-skills48k1 repos~2.5kAutomated safety check: NotesMIT
PacsomaticK-Dense-AI/scientific-agent-skills48k1 repos~1.6kAutomated safety check: PassMIT

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Works with

Categories

Questions about Merge Schemas

What does Merge Schemas do?

Regenerate nextflow.config and nextflowschema.json for Bactopia workflows by running bactopia-merge-schemas. Merge Schemas is an agent skill from bactopia/bactopia.json for Bactopia workflows by running bactopia-merge-schemas.

When should I use Merge Schemas?

Merge Schemas fits situations like: asked to merge schemas; regenerate workflow config; rebuild nextflowschema.json; sync workflow configs after module schema changes.

How do I install Merge Schemas in Claude Code?

Run `npx skills add bactopia/bactopia --skill merge-schemas -a claude-code`. Or copy the skill folder (.agents/skills/merge-schemas in bactopia/bactopia) into .claude/skills/merge-schemas in your project. Claude Code loads it when a task matches its description.

How do I install Merge Schemas in Codex?

Run `npx skills add bactopia/bactopia --skill merge-schemas -a codex`. Or copy the skill folder (.agents/skills/merge-schemas in bactopia/bactopia) into .agents/skills/merge-schemas in your project. Codex loads it when a task matches its description.

Can I use Merge Schemas in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add bactopia/bactopia --skill merge-schemas -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/merge-schemas, .gemini/skills/merge-schemas, .github/skills/merge-schemas and .opencode/skills/merge-schemas in your project.

What does Merge Schemas need to run?

Going by SKILL.md and its folder, Merge Schemas needs a shell for the scripts in its folder. Our summary lists: A Bash shell.

Does Merge Schemas access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Merge Schemas safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Merge Schemas use?

Merge Schemas is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Merge Schemas use?

About 1.3k tokens (SKILL.md is roughly 5k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Merge Schemas?

Skills that share tags, products or a category with Merge Schemas: LaminDB Biological Data Management (davila7/claude-code-templates, 32k stars), Latchbio Integration (davila7/claude-code-templates, 32k stars), Pacsomatic (BioTender-max/awesome-bio-agent-skills, 199 stars) and Latchbio Integration (K-Dense-AI/scientific-agent-skills, 48k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Merge Schemas?

bactopia (a GitHub organization) maintains it in bactopia/bactopia, which has 522 GitHub stars. The repository holds 15 skills in this directory. The repository was last updated on August 5, 2026.

Source: bactopia/bactopia on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.