Interview-Driven Workflow Construction and Repair in Galaxy

Ebola Virus Host RNA-seq Workflow Case Study

This directory contains the complete artifact bundle generated by the INTERVIEW → GALAXY pipeline (pipeline-interview-to-galaxy) from the Galaxy Workflow Foundry.

See CASE_STUDY.md for the complete phase audit, methodology, and results narrative.

Quick Links

• Generated Galaxy Workflow: galaxy-workflow.gxwf.yml
• Workflow Tests: galaxy-workflow.gxwf-tests.yml
• Test Plan: galaxy-test-plan.yml
• Test Data: test-data/
• Validation Report: galaxy-workflow-validation-result.json
• Test Execution Result: workflow-test-result.json
• HTML Test Report: tool_test_output.html
• Triage & Debug Report: workflow-debug-report.md

Re-running Verification

1. Static Validation

gxwf validate galaxy-workflow.gxwf.yml
gxwf validate-tests galaxy-workflow.gxwf-tests.yml --workflow galaxy-workflow.gxwf.yml
foundry validate-galaxy-workflow-test-plan galaxy-test-plan.yml

2. Planemo Execution with Docker Biocontainers

planemo test --biocontainers --test_output_json tool_test_output.json galaxy-workflow.gxwf.yml