Project Status

Project Status

Run the status script and interpret the output for the user.

Steps

1. Run bactopia-status via the wrapper script:

   bash .agents/skills/project-status/scripts/run-bactopia-status.sh --bactopia-path /home/rpetit3/repos/bactopia/bactopia --json
   

2. Parse 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)

3. 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

4. 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 generated
• repo — path to the Bactopia repository
• git — branch, commit, modified file count
• counts — modules, subworkflows, workflows
• tiers — per-tier detail, each with total, doc_count, issues[], tag_coverage
  • tag_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, or deprecated
• @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 @modules is 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