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 skills add broadinstitute/fiss-mcp --skill navigate-subworkflowsgit 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/navigate-subworkflows)<a href="https://agentmods.dev/skills/broadinstitute/fiss-mcp/navigate-subworkflows"><img src="https://agentmods.dev/badge/skills/broadinstitute/fiss-mcp/navigate-subworkflows/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/broadinstitute/fiss-mcp/navigate-subworkflows"><img src="https://agentmods.dev/badge/skills/broadinstitute/fiss-mcp/navigate-subworkflows.svg" alt="Reviewed on agentmods" width="80" 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 | $0.00033 | $0.01072 |
| Opus 5 | $0.00016 | $0.00536 |
| Sonnet 5 | $0.00007 | $0.00214 |
| Haiku 4.5 | $0.00003 | $0.00107 |
Grade A, and why
navigate-subworkflows 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 7d 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 — 179 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Navigating Subworkflows
This skill teaches you how to work with nested WDL subworkflows in Terra. When a WDL workflow calls another workflow (a subworkflow), each subworkflow gets its own workflow ID and can be inspected independently.
Understanding Subworkflows
In WDL, a workflow can call other workflows as tasks. When this happens:
- Parent workflow: Has its own workflow ID and metadata
- Subworkflow: Gets a separate workflow ID, visible in parent metadata
- Each subworkflow: Can be queried independently using Terra tools
Finding Subworkflow IDs
Subworkflow IDs are stored in the parent workflow's metadata under:
calls.<subworkflow_name>[*].subWorkflowId
Step 1: Get Parent Workflow Metadata
get_job_metadata(
workspace_namespace, workspace_name, submission_id, workflow_id,
mode="extract",
field_path="calls.*.subWorkflowId"
)
This returns subworkflow IDs for all task calls that are subworkflows.
Step 2: Identify Which Tasks Are Subworkflows
Not all tasks are subworkflows. To check:
get_job_metadata(
workspace_namespace, workspace_name, submission_id, workflow_id,
mode="summary"
)
In the summary, subworkflow tasks will have execution entries with subWorkflowId fields.
Alternative: Extract Specific Subworkflow ID
If you know the subworkflow task name:
get_job_metadata(
workspace_namespace, workspace_name, submission_id, workflow_id,
mode="extract",
task_name="my_subworkflow_call",
field_path="subWorkflowId"
)
Debugging Subworkflows
Once you have a subworkflow ID, use it directly with any workflow tool:
Get Subworkflow Summary
get_job_metadata(
workspace_namespace, workspace_name, submission_id,
workflow_id="<subworkflow-id>", # Use subworkflow ID here
mode="summary"
)
Get Subworkflow Logs
get_workflow_logs(
workspace_namespace, workspace_name, submission_id,
workflow_id="<subworkflow-id>",
fetch_content=True
)
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.
- 7d ago Changed · +7 lines 144c69332f12
- 11d ago First seen · 172 lines · 33 tokens per session scan A 813596f5d964
navigate-subworkflows is a skill published in the GitHub repository broadinstitute/fiss-mcp (5 stars, last pushed 7d ago), licensed Apache-2.0. It adds 33 tokens to every session and 1,072 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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