biokit-tasks

name	biokit-tasks
description	Generate an actionable, dependency-ordered tasks.md for the feature based on available design artifacts.
compatibility	Requires spec-kit project structure with .specify/ directory
metadata	{"author":"github-spec-kit","source":"templates/commands/tasks.md"}

Bioinfo SDD Contract

This skill keeps the upstream Spec Kit-style Codex invocation, but generated tasks must execute the Bioinfo SDD plan. Keep the strict Spec Kit checklist format while tying work to section artifacts, section.yml, gates, section-local installed_refs/, wrappers, adapters, deterministic checks, and evidence. Concrete tools remain inactive in tool_market/ until installed for the current section.

User Input

$ARGUMENTS

You MUST consider the user input before proceeding (if not empty).

Pre-Execution Checks

Check for extension hooks (before tasks generation):

• Check if .specify/extensions.yml exists in the project root.
• If it exists, read it and look for entries under the hooks.before_tasks key
• If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
• Filter out hooks where enabled is explicitly false. Treat hooks without an enabled field as enabled by default.
• For each remaining hook, do not attempt to interpret or evaluate hook condition expressions:
  • If the hook has no condition field, or it is null/empty, treat the hook as executable
  • If the hook defines a non-empty condition, skip the hook and leave condition evaluation to the HookExecutor implementation
• When constructing slash commands from hook command names, replace dots (.) with hyphens (-). For example, biokit.git.commit → /biokit-git-commit.
• For each executable hook, output the following based on its optional flag:
  • Optional hook (optional: true):

    ## Extension Hooks
    
    **Optional Pre-Hook**: {extension}
    Command: `/{command}`
    Description: {description}
    
    Prompt: {prompt}
    To execute: `/{command}`
    

  • Mandatory hook (optional: false):

    ## Extension Hooks
    
    **Automatic Pre-Hook**: {extension}
    Executing: `/{command}`
    EXECUTE_COMMAND: {command}
    
    Wait for the result of the hook command before proceeding to the Outline.
    

• If no hooks are registered or .specify/extensions.yml does not exist, skip silently

Outline

1. Setup: Run .specify/scripts/bash/setup-tasks.sh --json from repo root and parse FEATURE_DIR, TASKS_TEMPLATE, and AVAILABLE_DOCS list. FEATURE_DIR and TASKS_TEMPLATE must be absolute paths when provided. AVAILABLE_DOCS is a list of document names/relative paths available under FEATURE_DIR (for example research.md or contracts/). For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'''m Groot' (or double-quote if possible: "I'm Groot").

2. Load design documents: Read from FEATURE_DIR:

   • Required: plan.md (tech stack, libraries, structure), spec.md (user stories with priorities)
   • Optional: data-model.md (entities), contracts/ (interface contracts), research.md (decisions), quickstart.md (test scenarios)
   • Note: Not all projects have all documents. Generate tasks based on what's available.

3. Execute task generation workflow:

   • Load plan.md and extract tech stack, libraries, project structure
   • Load spec.md and extract user stories with their priorities (P1, P2, P3, etc.)
   • If data-model.md exists: Extract entities and map to user stories
   • If contracts/ exists: Map interface contracts to user stories
   • If research.md exists: Extract decisions for setup tasks
   • Generate tasks organized by user story (see Task Generation Rules below)
   • Generate dependency graph showing user story completion order
   • Create parallel execution examples per user story
   • Validate task completeness (each user story has all needed tasks, independently testable)

4. Generate tasks.md: Read the tasks template from TASKS_TEMPLATE (from the JSON output above) and use it as structure. If TASKS_TEMPLATE is empty, fall back to .specify/templates/tasks-template.md. Fill with:

   • Correct feature name from plan.md
   • Phase 1: Setup tasks (project initialization)
   • Phase 2: Foundational tasks (blocking prerequisites for all user stories)
   • Phase 3+: One phase per user story (in priority order from spec.md)
   • Each phase includes: story goal, independent test criteria, tests (if requested), implementation tasks
   • Final Phase: Polish & cross-cutting concerns
   • All tasks must follow the strict checklist format (see Task Generation Rules below)
   • Clear file paths for each task
   • Dependencies section showing story completion order
   • Parallel execution examples per story
   • Implementation strategy section (MVP first, incremental delivery)

5. Report: Output path to generated tasks.md and summary:

   • Total task count
   • Task count per user story
   • Parallel opportunities identified
   • Independent test criteria for each story
   • Suggested MVP scope (typically just User Story 1)
   • Format validation: Confirm ALL tasks follow the checklist format (checkbox, ID, labels, file paths)

6. Check for extension hooks: After tasks.md is generated, check if .specify/extensions.yml exists in the project root.

   • If it exists, read it and look for entries under the hooks.after_tasks key
   • If the YAML cannot be parsed or is invalid, skip hook checking silently and continue normally
   • Filter out hooks where enabled is explicitly false. Treat hooks without an enabled field as enabled by default.
   • For each remaining hook, do not attempt to interpret or evaluate hook condition expressions:
     • If the hook has no condition field, or it is null/empty, treat the hook as executable
     • If the hook defines a non-empty condition, skip the hook and leave condition evaluation to the HookExecutor implementation
   • When constructing slash commands from hook command names, replace dots (.) with hyphens (-). For example, biokit.git.commit → /biokit-git-commit.
   • For each executable hook, output the following based on its optional flag:
     • Optional hook (optional: true):

       ## Extension Hooks
       
       **Optional Hook**: {extension}
       Command: `/{command}`
       Description: {description}
       
       Prompt: {prompt}
       To execute: `/{command}`
       

     • Mandatory hook (optional: false):

       ## Extension Hooks
       
       **Automatic Hook**: {extension}
       Executing: `/{command}`
       EXECUTE_COMMAND: {command}
       

   • If no hooks are registered or .specify/extensions.yml does not exist, skip silently

Context for task generation: $ARGUMENTS

The tasks.md should be immediately executable - each task must be specific enough that an LLM can complete it without additional context.

Task Generation Rules

CRITICAL: Tasks MUST be organized by user story to enable independent implementation and testing.

Tests are OPTIONAL: Only generate test tasks if explicitly requested in the feature specification or if user requests TDD approach.

Checklist Format (REQUIRED)

Every task MUST strictly follow this format:

- [ ] [TaskID] [P?] [Story?] Description with file path

Format Components:

1. Checkbox: ALWAYS start with - [ ] (markdown checkbox)
2. Task ID: Sequential number (T001, T002, T003...) in execution order
3. [P] marker: Include ONLY if task is parallelizable (different files, no dependencies on incomplete tasks)
4. [Story] label: REQUIRED for user story phase tasks only
   • Format: [US1], [US2], [US3], etc. (maps to user stories from spec.md)
   • Setup phase: NO story label
   • Foundational phase: NO story label
   • User Story phases: MUST have story label
   • Polish phase: NO story label
5. Description: Clear action with exact file path

Examples:

• ✅ CORRECT: - [ ] T001 Create project structure per implementation plan
• ✅ CORRECT: - [ ] T005 [P] Implement authentication middleware in src/middleware/auth.py
• ✅ CORRECT: - [ ] T012 [P] [US1] Create User model in src/models/user.py
• ✅ CORRECT: - [ ] T014 [US1] Implement UserService in src/services/user_service.py
• ❌ WRONG: - [ ] Create User model (missing ID and Story label)
• ❌ WRONG: T001 [US1] Create model (missing checkbox)
• ❌ WRONG: - [ ] [US1] Create User model (missing Task ID)
• ❌ WRONG: - [ ] T001 [US1] Create model (missing file path)

Task Organization

1. From User Stories (spec.md) - PRIMARY ORGANIZATION:

   • Each user story (P1, P2, P3...) gets its own phase
   • Map all related components to their story:
     • Models needed for that story
     • Services needed for that story
     • Interfaces/UI needed for that story
     • If tests requested: Tests specific to that story
   • Mark story dependencies (most stories should be independent)

2. From Contracts:

   • Map each interface contract → to the user story it serves
   • If tests requested: Each interface contract → contract test task [P] before implementation in that story's phase

3. From Data Model:

   • Map each entity to the user story(ies) that need it
   • If entity serves multiple stories: Put in earliest story or Setup phase
   • Relationships → service layer tasks in appropriate story phase

4. From Setup/Infrastructure:

   • Shared infrastructure → Setup phase (Phase 1)
   • Foundational/blocking tasks → Foundational phase (Phase 2)
   • Story-specific setup → within that story's phase

Phase Structure

• Phase 1: Setup (project initialization)
• Phase 2: Foundational (blocking prerequisites - MUST complete before user stories)
• Phase 3+: User Stories in priority order (P1, P2, P3...)
  • Within each story: Tests (if requested) → Models → Services → Endpoints → Integration
  • Each phase should be a complete, independently testable increment
• Final Phase: Polish & Cross-Cutting Concerns