clinical-trial-protocol-full-workflow-logic

name	clinical-trial-protocol-full-workflow-logic
description	Sub-skill of clinical-trial-protocol: Full Workflow Logic.
version	1.0.0
category	science
type	reference
scripts_exempt	true

Full Workflow Logic

Full Workflow Logic

Step 1: Check for Existing Waypoints

• If waypoints/intervention_metadata.json exists: Load metadata, check completed_steps array, resume from next incomplete step
• If no metadata exists: Start from Step 0

Step 2: Execute Steps in Order

For each step (0, 1, 2, 3, 4, 5):

1. Check completion status: If step already completed in metadata, skip with "Step [X] already complete"

2. Execute step: Display "Executing Step [X]...", read and follow the corresponding subskill file instructions, wait for completion, display "Step [X] complete"

   • Step execution method (ON-DEMAND LOADING): When a step is ready to execute (NOT before), read the subskill markdown file and execute ALL instructions within it
   • IMPORTANT: Do NOT read subskill files in advance. Only read them at the moment of execution.
   • Step-to-file mapping:
     • Step 0: references/00-initialize-intervention.md (read when Step 0 executes)
     • Step 1: references/01-research-protocols.md (read when Step 1 executes)
     • Step 2: references/02-protocol-foundation.md (read when Step 2 executes - sections 1-6)
     • Step 3: references/03-protocol-intervention.md (read when Step 3 executes - sections 7-8)
     • Step 4: references/04-protocol-operations.md (read when Step 4 executes - sections 9-12)
     • Step 5: references/05-concatenate-protocol.md (read when Step 5 executes - final concatenation)

3. Handle errors: If step fails, ask user to retry or exit. Save current state for resume capability.

4. Display progress: "Progress: [X/6] steps complete", show estimated remaining time

5. Step 4 Completion Pause: After Step 4 completes, pause and display the Protocol Completion Menu (see below). Wait for user selection before proceeding.

Step 2.5: Protocol Completion Menu

After Step 4 completes successfully, display the EXACT menu below (do not improvise or create alternative options):

PROTOCOL COMPLETE: Protocol Draft Generated

Protocol Details:
  - Study Design: [Design from metadata]
  - Sample Size: [N subjects from metadata]
  - Primary Endpoint: [Endpoint from metadata]
  - Study Duration: [Duration from metadata]

Protocol file: waypoints/02_protocol_draft.md
File size: [Size in KB]

WHAT WOULD YOU LIKE TO DO NEXT?

1. Review Protocol in Artifact - click on the .md file above

2. Concatenate Final Protocol (Step 5)

3. Exit and Review Later

Option 1 Logic (Review in Artifact): Pause, let user open the section files, wait for further instruction

Option 2 Logic (Concatenate Protocol):

1. Execute Step 5 by reading and following references/05-concatenate-protocol.md
2. Step 5 will concatenate all section files into final protocol document
3. Continue to Step 3 (Final Summary) after Step 5 completes

Option 3 Logic (Exit):

1. Display: "Protocol sections saved. You can resume with Step 5 anytime to concatenate."
2. Exit orchestrator gracefully

Step 3: Final Summary

Display completion message with:

• Intervention name, type (device/drug), indication
• Protocol details (design, sample size, endpoints, duration)
• All completed steps list
• Final deliverable: Complete protocol markdown file location (waypoints/protocol_complete.md)
• Waypoint files list for reference
• Important disclaimers (FDA Pre-Sub, biostatistician review, IRB approval required)
• Thank you message