| name | skill-epi-research |
| description | Research skill for epidemiology study design and analysis planning. Invoke for epi/epi:study research tasks. |
| allowed-tools | Agent, Bash, Edit, Read, Write, AskUserQuestion |
Epi Research Skill
Thin wrapper that delegates epidemiology research to epi-research-agent subagent.
IMPORTANT: This skill implements the skill-internal postflight pattern. After the subagent returns,
this skill handles all postflight operations (status update, artifact linking, git commit) before returning.
Context References
Reference (do not load eagerly):
- Path:
.claude/context/formats/return-metadata-file.md - Metadata file schema
- Path:
.claude/context/patterns/postflight-control.md - Marker file protocol
- Path:
.claude/context/patterns/file-metadata-exchange.md - File I/O helpers
- Path:
.claude/context/patterns/jq-escaping-workarounds.md - jq escaping patterns (Issue #1132)
Note: This skill is a thin wrapper with internal postflight. Context is loaded by the delegated agent.
Trigger Conditions
This skill activates when:
/research on a task with task_type: "epi" or task_type: "epi:study"- Epidemiology extension is available
Input Parameters
Required Parameters
task_number - Task number (must exist in state.json with task_type="epi" or "epi:study")session_id - Session ID from orchestrator
Execution Flow
Stage 1: Input Validation
Validate required inputs:
task_number - Must be provided and exist in state.json- Verify task_type is "epi" or "epi:study"
task_data=$(jq -r --argjson num "$task_number" \
'.active_projects[] | select(.project_number == $num)' \
specs/state.json)
if [ -z "$task_data" ]; then
return error "Task $task_number not found"
fi
task_type=$(echo "$task_data" | jq -r '.task_type // ""')
status=$(echo "$task_data" | jq -r '.status')
project_name=$(echo "$task_data" | jq -r '.project_name')
description=$(echo "$task_data" | jq -r '.description // ""')
if [ "$task_type" = "epi" ] || [ "$task_type" = "epi:study" ]; then
:
else
return error "Task $task_number is not an epi task (task_type=$task_type)"
fi
Stage 2 + Stage 3: Preflight Status Update and Postflight Marker
Source skill-base.sh once, then follow @.claude/context/patterns/skill-preflight-flow.md in
full for Stage 2 (preflight status update) and Stage 3 (marker creation):
source .claude/scripts/skill-base.sh
padded_num=$(printf "%03d" "$task_number")
skill_name="skill-epi-research"
operation="research"
operation="research" (not "epi_research") is required here: update-task-status.sh's
target_status vocabulary has no epi_research value, so this skill maps onto the plain
research operation, same as skill-researcher. The marker's operation field now reads
"research" rather than "epi_research" — a byte-for-byte Shape A key set, matching what this
skill's marker already carried (created, stop_hook_active) before this conversion.
Stage 4a: Memory Retrieval and Literature Detection
Skip memory retrieval if: clean_flag is true (from --clean).
if [ "$clean_flag" != "true" ]; then
memory_context=$(bash .claude/scripts/memory-retrieve.sh "$description" "$task_type" "" 2>/dev/null) || memory_context=""
fi
Follow @.claude/context/patterns/lit-stage4a-flow.md in full to resolve --lit and set
lit_context, exactly as skill-researcher does. This skill supplies the shared block's
preconditions: lit_flag, description, orchestrator_mode (default "false" when unset).
Stage 4: Prepare Delegation Context
{
"session_id": "sess_{timestamp}_{random}",
"delegation_depth": 1,
"delegation_path": ["orchestrator", "research", "skill-epi-research"],
"timeout": 3600,
"task_context": {
"task_number": N,
"task_name": "{project_name}",
"description": "{description}",
"task_type": "{task_type}"
},
"workflow_type": "epi_research",
"forcing_data": "{from state.json task metadata: study_design, data_paths, etc.}",
"metadata_file_path": "specs/{NNN}_{SLUG}/.return-meta.json"
}
Stage 5: Invoke Subagent
CRITICAL: Use the Agent tool to spawn the subagent.
Tool: Agent (NOT Skill, NOT Plan)
Parameters:
- subagent_type: "epi-research-agent"
- prompt: [Include task_context, delegation_context, workflow_type, forcing_data, metadata_file_path]
- description: "Execute epi_research for task {N}"
DO NOT use Skill(epi-research-agent) - this will FAIL.
Stage 5b: Self-Execution Fallback
CRITICAL: If you performed the work above WITHOUT using the Agent tool (i.e., you read files,
wrote artifacts, or updated metadata directly instead of spawning a subagent), you MUST write a
.return-meta.json file now before proceeding to postflight. Use the schema from
return-metadata-file.md with the appropriate status value for this operation.
If you DID use the Agent tool, skip this stage -- the subagent already wrote the metadata.
Postflight (ALWAYS EXECUTE)
The following stages MUST execute after work is complete, whether the work was done by a
subagent or inline (Stage 5b). Do NOT skip these stages for any reason.
Stage 6: Read Metadata File
metadata_file="specs/${padded_num}_${project_name}/.return-meta.json"
if [ -f "$metadata_file" ] && jq empty "$metadata_file" 2>/dev/null; then
status=$(jq -r '.status' "$metadata_file")
artifact_path=$(jq -r '.artifacts[0].path // ""' "$metadata_file")
artifact_type=$(jq -r '.artifacts[0].type // "report"' "$metadata_file")
artifact_summary=$(jq -r '.artifacts[0].summary // ""' "$metadata_file")
memory_candidates=$(jq -c '.memory_candidates // []' "$metadata_file")
else
echo "Error: Invalid or missing metadata file"
status="failed"
fi
Note: renamed the local variable from meta_status to status to match the
skill-postflight-flow.md shared block's precondition naming used below.
Stage 7, 7a, 8, 8a: Postflight Status, Memory Candidates, Artifact Linking, Notify
MUST NOT cross the postflight boundary: The subagent MUST NOT update state.json or TODO.md status.
Only this skill performs postflight status transitions.
Follow @.claude/context/patterns/skill-postflight-flow.md for Stage 7 (postflight status
update), Stage 7a (memory-candidate propagation), Stage 8 (artifact linking; artifact type
"report", a study design report), and Stage 8a (TTS notify):
field_name='**Research**'
next_field='**Plan**'
skill_postflight_update "$task_number" "$operation" "$session_id" "$status"
skill_propagate_memory_candidates "$task_number" "$memory_candidates" "$session_id"
skill_link_artifacts "$task_number" "$artifact_path" "$artifact_type" "$artifact_summary" \
"$field_name" "$next_field" "$session_id"
skill_lifecycle_notify "$status"
| status | Final state.json | Final TODO.md |
|---|
| researched | researched | [RESEARCHED] |
| partial | researching (unchanged — skill_postflight_update no-ops) | [RESEARCHING] |
| failed | (keep preflight, unchanged) | (keep preflight marker) |
Stage 9: Git Commit
Apply the research scope from .claude/context/standards/git-staging-scope.md — targeted
staging, never a repo-wide add:
git add \
"specs/${padded_num}_${project_name}/reports/" \
"specs/${padded_num}_${project_name}/.return-meta.json" \
"specs/TODO.md" \
"specs/state.json"
git commit -m "task ${task_number}: complete epi research
Session: ${session_id}"
Stage 10: Cleanup
Follow @.claude/context/patterns/skill-postflight-flow.md's Stage 9 (cleanup):
skill_cleanup "$padded_num" "$project_name"
Stage 11: Return Brief Summary
Research Success:
Epi research completed for task {N}:
- Study design and analysis plan documented
- Created report at specs/{NNN}_{SLUG}/reports/{MM}_epi-research.md
- Status updated to [RESEARCHED]
- Changes committed with session {session_id}
Error Handling
Task not found
Epi research skill error for task {N}:
- Task not found in state.json
- No status changes made
Wrong task_type
Epi research skill error for task {N}:
- Task is not an epi task (task_type={task_type})
- No status changes made
Metadata file missing
Keep status at preflight level for resume.
Git commit failure
Non-blocking. Log failure but continue.
Return Format
This skill returns a brief text summary (NOT JSON). The JSON metadata is written to the file and processed internally.
