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Agent skill

Bump Versions

by bactopia in bactopia/bactopia

Propagate the Bactopia and nf-bactopia versions declared in versions.yml into the hand-maintained files that carry a literal version (conf/testbase.config, CITATION.cff, bin/bactopia…

MITAuto-check passedResearch & Science

Install Bump Versions

skills CLI
$ npx skills add bactopia/bactopia --skill bump-versions -a claude-code

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

GitHub CLI
$ gh skill install bactopia/bactopia bump-versions --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/bump-versions .claude/skills/bump-versions && 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
bump-versions
GitHub stars
522
Token cost
~1.3k tokens
SKILL.md length
519 words
Files
3 (incl. scripts)
Skills in repo
15
Repo updated
First seen
Licence
MIT

At a glance

Propagate the Bactopia and nf-bactopia versions declared in versions.yml into the hand-maintained files that carry a literal version (conf/testbase.config, CITATION.cff, bin/bactopia…

  • Works in 5 steps: Dry-run first. Show the user exactly… → Confirm, then apply. Once the user is… → Recommend the regeneration follow-ups.… → …
  • Has edited versions.yml and wants the rest of the repo brought in line
  • SKILL.md covers Steps and Notes
  • Runs Python scripts from its folder; calls python3 and bash

What it does

Bump Versions is an agent skill from bactopia/bactopia. Propagate the Bactopia and nf-bactopia versions declared in versions.yml into the hand-maintained files that carry a literal version (conf/testbase.config, CITATION.cff, bin/bactopia, data/conda/meta.yaml). Use this whenever the user has edited versions.yml and wants the rest of the repo brought in line, or asks to bump the version, set the release version, propagate versions.yml, sync version-bearing files, fix a V001 version-consistency failure, or prepare version files for a release. This never edits…

Its SKILL.md is about 1.3k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files, including scripts (for example `evals/evals.json` and `scripts/bump_versions.py`).

It sits in Research & Science, covering Reproducible research and Citation management. 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

  • Has edited versions.yml and wants the rest of the repo brought in line
  • Asks to bump the version
  • Set the release version
  • Propagate versions.yml

Example prompts

  • “/bump-versions”

Requirements

  • Python 3

Workflow steps

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

  1. Dry-run first. Show the user exactly what will change before writing anything
  2. Confirm, then apply. Once the user is happy with the dry-run, drop --check
  3. Recommend the regeneration follow-ups. If anything changed (or a generated
  4. Verify V001–V003. Confirm the version gate is actually green
  5. Flag downstream checks (report, don't fix)

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/ (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python3
    • bash

    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

Bump Versions loads about 1.3k tokens when it runs. Until then it costs about 170 tokens; SKILL.md has 519 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~170
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). 519 words, ~1,259 tokens.

Download SKILL.mdSave it as .claude/skills/bump-versions/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.
name
bump-versions
description
Propagate the Bactopia and nf-bactopia versions declared in versions.yml into the hand-maintained files that carry a literal version (conf/test_base.config, CITATION.cff, bin/bactopia, data/conda/meta.yaml). Use this whenever the user has edited versions.yml and wants the rest of the repo brought in line, or asks to bump the version, set the release version, propagate versions.yml, sync version-bearing files, fix a V001 version-consistency failure, or prepare version files for a release. This never edits versions.yml itself and never regenerates the templated artifacts (nextflow.config, catalog.json) — it hands those off to /merge-schemas and /update-catalog.

Bump Versions

versions.yml at the repo root is the single source of truth for the pipeline version (bactopia) and the plugin pin (nf-bactopia). It is edited by hand — this skill never touches it. Its job is the mechanical, error-prone part: copying those two values into every hand-maintained file that repeats them, so bactopia-lint's V001 (version-bearing files must equal versions.yml) goes green.

Two classes of version-bearing files exist, and only one is this skill's concern:

  • Hand-maintained (this skill fixes these): conf/test_base.config (bactopia_version + the nf-bactopia@ plugin pin, inherited by all ~183 module/subworkflow test configs), CITATION.cff, bin/bactopia, data/conda/meta.yaml.
  • Generated (this skill does NOT touch these): nextflow.config, every workflows/*/nextflow.config, catalog.json, llms.txt. These are rendered from versions.yml by bactopia-merge-schemas / bactopia-catalog, so the fix is to regenerate them — a follow-up, not an edit. Slash commands cannot invoke other slash commands, so you recommend those to the user rather than running them.

Steps

  1. Dry-run first. Show the user exactly what will change before writing anything:

    python3 .agents/skills/bump-versions/scripts/bump_versions.py \
    --bactopia-path /home/rpetit3/repos/bactopia/bactopia --check

    The script reads versions.yml, then reports each hand-maintained literal as would update <old> -> <new>, already <value>, or a WARN (file missing or the literal moved). If everything is already ok, tell the user the hand-maintained files are in sync and skip to step 4 (they may still need a regen if a generated artifact lagged).

  2. Confirm, then apply. Once the user is happy with the dry-run, drop --check to write the changes:

    python3 .agents/skills/bump-versions/scripts/bump_versions.py \
    --bactopia-path /home/rpetit3/repos/bactopia/bactopia

    Only the version token inside each match is rewritten; runs are idempotent.

  3. Recommend the regeneration follow-ups. If anything changed (or a generated artifact is suspected stale), tell the user to run, in order:

    • /merge-schemas all — re-renders nextflow.config + workflow configs + schemas from versions.yml.
    • /update-catalog — rebuilds catalog.json + llms.txt. Do not attempt to run these from here.

  4. Verify V001–V003. Confirm the version gate is actually green:

    bash .agents/skills/review-groovydoc/scripts/run-bactopia-lint.sh \
    --bactopia-path /home/rpetit3/repos/bactopia/bactopia --json --silent

    Read the repo component's results. A clean run lists no V0xx failures (PASS results are suppressed). If V001 still fails, report the offending files verbatim — most often a generated artifact whose regen (step 3) hasn't run yet, or a version-bearing file this skill doesn't own.

  5. Flag downstream checks (report, don't fix):

    • V002 compares versions.yml to the top ## vX.Y.Z CHANGELOG heading. If they disagree, the CHANGELOG needs a section for the new version — that's human-authored content, so surface it, don't invent it.
    • Bumping bactopia_version changes the test container tag (bactopia/bactopia:<version>) used by every module/subworkflow test. Recommend a smoke test (/run-tests on a quick component) once the matching image exists, since a nonexistent tag will fail tests even with a green lint.
Show full SKILL.md (101 more words)Show less

Notes

  • The script needs only Python stdlib + read access to versions.yml; no conda env or bactopia-* CLI. There is deliberately no bactopia-versions CLI — versions.yml is hand-edited and this propagation is the whole story.
  • The four hand-maintained targets and their literal formats are encoded in the script's TARGETS map, matching V001's own regexes so the skill fixes exactly what the linter checks. If V001 ever grows a new hand-maintained file, add it there.
Sibling skills
  • /merge-schemas, /update-catalog — the regeneration follow-ups (step 3).
  • /review-groovydoc — backs the bactopia-lint verification run (step 4).
  • /release-checklist — its check 1 delegates the version gate to these same V-rules.

© 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 2 other files (scripts) in .agents/skills/bump-versions of bactopia/bactopia.

  • SKILL.md
  • evals/evals.json
  • scripts/bump_versions.py

Open the folder on GitHubat commit 29fb741

Compare with similar skills

Bump Versions 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.

Bump Versions compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Bump Versions this skillbactopia/bactopia522—~1.3kAutomated safety check: PassMIT
Peer ReviewK-Dense-AI/claude-scientific-writer2.4k2 repos~3.1kAutomated safety check: NotesMIT
Literature ReviewK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: NotesMIT
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-skills197—~1.3kAutomated safety check: PassMIT

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  • Release Checklist

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    Audit whether Bactopia is ready for a version release and produce a GO / NO-GO recommendation report.

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  • Review Citations

    bactopia/bactopia

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  • Review Docs

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Works with

Categories

Questions about Bump Versions

What does Bump Versions do?

Propagate the Bactopia and nf-bactopia versions declared in versions.yml into the hand-maintained files that carry a literal version (conf/testbase.config, CITATION.cff, bin/bactopia…. Bump Versions is an agent skill from bactopia/bactopia.yaml).

When should I use Bump Versions?

Bump Versions fits situations like: has edited versions.yml and wants the rest of the repo brought in line; asks to bump the version; set the release version; propagate versions.yml.

How do I install Bump Versions in Claude Code?

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

How do I install Bump Versions in Codex?

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

Can I use Bump Versions 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 bump-versions -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bump-versions, .gemini/skills/bump-versions, .github/skills/bump-versions and .opencode/skills/bump-versions in your project.

What does Bump Versions need to run?

Going by SKILL.md and its folder, Bump Versions needs Python for the scripts in its folder and the command-line tools its instructions call (python3 and bash). Our summary lists: Python 3.

Does Bump Versions 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 Bump Versions 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 Bump Versions use?

Bump Versions 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 Bump Versions 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 Bump Versions?

Skills that share tags, products or a category with Bump Versions: Peer Review (K-Dense-AI/claude-scientific-writer, 2.4k stars), Literature Review (K-Dense-AI/scientific-agent-skills, 48k stars), LaminDB Biological Data Management (davila7/claude-code-templates, 32k stars) and Latchbio Integration (davila7/claude-code-templates, 32k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Bump Versions?

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.