Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add skills/broadinstitute/fiss-mcp/debug-workflow-failurenpx skills add broadinstitute/fiss-mcp --skill debug-workflow-failuregit clone --depth 1 https://github.com/broadinstitute/fiss-mcpWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/broadinstitute/fiss-mcp/debug-workflow-failure)<a href="https://agentmods.dev/skills/broadinstitute/fiss-mcp/debug-workflow-failure"><img src="https://agentmods.dev/badge/skills/broadinstitute/fiss-mcp/debug-workflow-failure.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00035 | $0.00928 |
| Opus 5 | $0.00017 | $0.00464 |
| Sonnet 5 | $0.00007 | $0.00186 |
| Haiku 4.5 | $0.00003 | $0.00093 |
Grade A, and why
debug-workflow-failure scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 6d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 121 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Debugging Workflow Failures in Terra
This skill teaches you how to efficiently debug failed Terra workflow submissions without exhausting your context window.
Efficient Debugging Sequence
Follow this sequence to minimize context usage while maximizing diagnostic information:
Step 1: Get Submission Overview
get_submission_status(workspace_namespace, workspace_name, submission_id)
This returns:
- Overall submission status
- Count of workflows by status (Succeeded, Failed, Running)
- List of workflow IDs with their individual statuses
What to look for: Identify failed workflow IDs from the status_summary and workflows array.
Step 2: Get Failed Task Details (~1-2K tokens)
get_job_metadata(workspace_namespace, workspace_name, submission_id, workflow_id, mode="summary")
The summary mode returns a context-efficient view with:
- Workflow status and timing
- Task counts by execution status
- Failed task details with error messages
- Log URLs for failed tasks
What to look for: The failed_tasks array contains task names, shard indices, error messages, and log URLs.
Step 3: Get Log URLs (fast, small response)
get_workflow_logs(workspace_namespace, workspace_name, submission_id, workflow_id, fetch_content=False)
Returns GCS URLs for stderr/stdout without fetching content. Use this to identify which logs exist before deciding what to fetch.
Step 4: Fetch Specific Failed Task Logs
Only fetch logs for tasks you need to debug:
get_workflow_logs(workspace_namespace, workspace_name, submission_id, workflow_id, fetch_content=True)
Logs are automatically truncated (first 5K + last 20K chars) to preserve error messages while staying context-efficient.
Step 5: Check Infrastructure Issues (if needed)
If stderr logs don't explain the failure, check for infrastructure issues:
get_batch_job_status(workspace_namespace, workspace_name, submission_id, workflow_id, task_name)
Signs you need this tool:
- Task failed but stderr is empty or very short
- Error says "The job was stopped before the command finished"
- Batch reports exit code 0 but task is marked Failed
- Task failed instantly (0 seconds runtime)
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 6d ago First seen · 121 lines · 35 tokens per session scan A 666438974bd3
debug-workflow-failure is a skill published in the GitHub repository broadinstitute/fiss-mcp (5 stars, last pushed 3d ago), licensed Apache-2.0. It adds 35 tokens to every session and 928 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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