Requirements
rizsotto/Bear
Write, modify, or review a requirement file under docs/requirements -- pick the single owning file, keep the text contract-only, name IDs so they need no explanation, and verify cross-references and…
Show a live snapshot of the Bactopia project state — component counts, GroovyDoc coverage, nf-test coverage, and structural issues.
Install Project Status
$ npx skills add bactopia/bactopia --skill project-status -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bactopia/bactopia project-status --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/bactopia/bactopia.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.agents/skills/project-status .claude/skills/project-status && rm -rf skills-srcUse ~/.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/
Install the "project-status" agent skill from https://github.com/bactopia/bactopia/tree/master/.agents/skills/project-status into .claude/skills/project-status/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "project-status", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/bactopia/bactopia/tree/master/.agents/skills/project-statusType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add bactopia/bactopia --skill project-status -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bactopia/bactopia project-status --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bactopia/bactopia.git skills-src && mkdir -p .agents/skills && cp -r skills-src/.agents/skills/project-status .agents/skills/project-status && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "project-status" agent skill from https://github.com/bactopia/bactopia/tree/master/.agents/skills/project-status into .agents/skills/project-status/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "project-status", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add bactopia/bactopia --skill project-status -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bactopia/bactopia project-status --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bactopia/bactopia.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/.agents/skills/project-status .cursor/skills/project-status && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "project-status" agent skill from https://github.com/bactopia/bactopia/tree/master/.agents/skills/project-status into .cursor/skills/project-status/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "project-status", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/bactopia/bactopia.git --path .agents/skills/project-status--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add bactopia/bactopia --skill project-status -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bactopia/bactopia project-status --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bactopia/bactopia.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/.agents/skills/project-status .gemini/skills/project-status && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "project-status" agent skill from https://github.com/bactopia/bactopia/tree/master/.agents/skills/project-status into .gemini/skills/project-status/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "project-status", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install bactopia/bactopia project-statusInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add bactopia/bactopia --skill project-status -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/bactopia/bactopia.git skills-src && mkdir -p .github/skills && cp -r skills-src/.agents/skills/project-status .github/skills/project-status && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "project-status" agent skill from https://github.com/bactopia/bactopia/tree/master/.agents/skills/project-status into .github/skills/project-status/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "project-status", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add bactopia/bactopia --skill project-status -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install bactopia/bactopia project-status --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bactopia/bactopia.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/.agents/skills/project-status .opencode/skills/project-status && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "project-status" agent skill from https://github.com/bactopia/bactopia/tree/master/.agents/skills/project-status into .opencode/skills/project-status/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "project-status", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
project-status- GitHub stars
- 522
- Token cost
- ~787 tokens
- SKILL.md length
- 320 words
- Files
- 2 (incl. scripts)
- Skills in repo
- 15
- Repo updated
- First seen
- Licence
- MIT
At a glance
Show a live snapshot of the Bactopia project state — component counts, GroovyDoc coverage, nf-test coverage, and structural issues.
- Works in 4 steps: Run bactopia-status via the wrapper script → Parse the JSON output and present a… → Highlight the most important gaps —… → …
- Asked about project state
- SKILL.md covers Steps and Notes
- Runs Shell scripts from its folder; calls bash
What it does
Project Status is an agent skill from bactopia/bactopia. 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.
Its SKILL.md is about 790 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-status.sh`).
It sits in Testing & QA, covering Test coverage. The repository describes itself as: A flexible pipeline for complete analysis of bacterial genomes. The licence is MIT.
When your agent uses it
- Asked about project state
- Whats documented
- What needs attention
Example prompts
- “s missing, what”
- “/project-status”
Requirements
- A Bash shell
Workflow steps
4 steps, taken from the first numbered list in SKILL.md.
- Run bactopia-status via the wrapper script
- Parse the JSON output and present a clean, readable summary. Lead with
- Highlight the most important gaps — prioritize by
- If the user asks "what should I work on next?", suggest the highest-priority gaps from the output.
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.
Shell commands in SKILL.md call:
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
Project Status loads about 787 tokens when it runs. Until then it costs about 63 tokens; SKILL.md has 320 words of instructions outside code blocks.
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). 320 words, ~787 tokens.
Download SKILL.mdSave it as
.claude/skills/project-status/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.- name
- project-status
- description
- 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.
Project Status
Run the status script and interpret the output for the user.
Steps
Run
bactopia-statusvia the wrapper script:bash .agents/skills/project-status/scripts/run-bactopia-status.sh --bactopia-path /home/rpetit3/repos/bactopia/bactopia --jsonParse the JSON output and present a clean, readable summary. Lead with:
- Component counts (modules / subworkflows / workflows)
- GroovyDoc coverage per tier (doc_count vs total)
- Tag coverage per tier — highlight any required tags below 100%
- nf-test coverage (workflows only)
- Any structural issues (missing required files)
Highlight the most important gaps — prioritize by:
- Missing required files (module.config, schema.json) first — these are structural breaks
- Missing GroovyDoc second — documentation gaps
- Missing nf-tests last — coverage gaps
If the user asks "what should I work on next?", suggest the highest-priority gaps from the output.
Notes
- The wrapper script auto-discovers
bactopia-status(checks PATH, then conda envs) - nf-test coverage is workflows-only — modules and subworkflows are excluded for now
- Report whether the root pipeline test exists (
nftest.root_test)
JSON Output Fields
timestamp— when the report was generatedrepo— path to the Bactopia repositorygit—branch,commit,modifiedfile countcounts—modules,subworkflows,workflowstiers— per-tier detail, each withtotal,doc_count,issues[],tag_coveragetag_coverage— map of tag name to count of components that have it
nftest—total(workflow count),tested,root_test
GroovyDoc Fields
All components use these required tags:
@status—stable,beta, ordeprecated@keywords— comma-separated search terms@tags—complexity:<simple|moderate|complex> input-type:<single|multiple|parameter> output-type:<single|multiple> features:<list>@citation— comma-separated bibtex keys@note— optional caveats or requirements
Modules and subworkflows also use:
@input— input channel descriptions (can be multi-line for records)@output— output channel descriptions (single-line)
Subworkflows additionally use:
@subworkflows— list of included subworkflows (directory keys)@modules— list of included modules (directory keys)
Entry workflows use:
@subworkflows— included subworkflows (directory keys); workflows never call modules directly, so@modulesis not used@input— parameter inputs (e.g.,rundir)@section— groups published outputs@publish— file patterns with descriptions (within sections)@note— can appear at top level or within a section
Required Files per Tier
- Modules:
module.config,schema.json - Subworkflows: none beyond
main.nf - Workflows: none beyond
main.nf
© 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/project-status of bactopia/bactopia.
- SKILL.md
- scripts/run-bactopia-status.sh
Open the folder on GitHubat commit 29fb741
Compare with similar skills
Project Status 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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Project Status this skillbactopia/bactopia | 522 | — | ~787 | Automated safety check: Pass | MIT | |
| Requirementsrizsotto/Bear | 6.5k | — | ~2k | Automated safety check: Pass | GPL-3.0 | |
| Crap Analysisardalis/RiverBooks | 134 | 2 repos | ~3.4k | Automated safety check: Pass | None | |
| Code Coverages3s-project/s3s | 311 | — | ~789 | Automated safety check: Pass | Apache-2.0 | |
| Check Coverageldayton/Dippy | 243 | — | ~403 | Automated safety check: Pass | MIT | |
| Guarding Destructive Operationskajisho5/ffmpeg-skill | 1.9k | — | ~2.6k | Automated safety check: Pass | MIT |
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Related
Categories
Questions about Project Status
What does Project Status do?
Show a live snapshot of the Bactopia project state — component counts, GroovyDoc coverage, nf-test coverage, and structural issues. Project Status is an agent skill from bactopia/bactopia. Show a live snapshot of the Bactopia project state — component counts, GroovyDoc coverage, nf-test coverage, and structural issues.
When should I use Project Status?
Project Status fits situations like: asked about project state; whats documented; what needs attention.
How do I install Project Status in Claude Code?
Run `npx skills add bactopia/bactopia --skill project-status -a claude-code`. Or copy the skill folder (.agents/skills/project-status in bactopia/bactopia) into .claude/skills/project-status in your project. Claude Code loads it when a task matches its description.
How do I install Project Status in Codex?
Run `npx skills add bactopia/bactopia --skill project-status -a codex`. Or copy the skill folder (.agents/skills/project-status in bactopia/bactopia) into .agents/skills/project-status in your project. Codex loads it when a task matches its description.
Can I use Project Status 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 project-status -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/project-status, .gemini/skills/project-status, .github/skills/project-status and .opencode/skills/project-status in your project.
What does Project Status need to run?
Going by SKILL.md and its folder, Project Status needs a shell for the scripts in its folder and the command-line tools its instructions call (bash). Our summary lists: A Bash shell.
Does Project Status 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 Project Status 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 Project Status use?
Project Status 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 Project Status use?
About 787 tokens (SKILL.md is roughly 3.1k 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 Project Status?
Skills that share tags, products or a category with Project Status: Requirements (rizsotto/Bear, 6.5k stars), Crap Analysis (ardalis/RiverBooks, 134 stars), Code Coverage (s3s-project/s3s, 311 stars) and Check Coverage (ldayton/Dippy, 243 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Project Status?
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.