Borrowing it
Nothing to install: this file belongs to boettiger-lab/data-workflows. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/boettiger-lab/data-workflows/main/.claude/skills/armada-pipeline/SKILL.mdgit clone --depth 1 https://github.com/boettiger-lab/data-workflowsWrote 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/boettiger-lab/data-workflows/armada-pipeline)<a href="https://agentmods.dev/skills/boettiger-lab/data-workflows/armada-pipeline"><img src="https://agentmods.dev/badge/skills/boettiger-lab/data-workflows/armada-pipeline.svg" alt="Measured on agentmods" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 6 findings, up to high
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- high Supply Chain · line 85 Remote code is downloaded and executed. This bypasses code review and could introduce malicious code.Fix: Avoid downloading and executing remote scripts. Use trusted packages from PyPI/npm. If remote fetch is required, verify checksums and use HTTPS.
- high Privilege Escalation · line 102 Code accesses credential files (SSH keys, AWS credentials, etc.). This could indicate credential theft attempts.Fix: Remove references to credential paths. Use environment variables or secrets managers. For docs, use placeholder paths (e.g., /path/to/config). Never load .env or token files in production code paths.
- high Supply Chain · line 126 Remote code is downloaded and executed. This bypasses code review and could introduce malicious code.Fix: Avoid downloading and executing remote scripts. Use trusted packages from PyPI/npm. If remote fetch is required, verify checksums and use HTTPS.
- medium Data Exfiltration · line 85 Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
- medium Rogue Agent · line 95 Skill establishes unauthorized persistence across sessions via cron jobs, startup scripts, or state files. Session persistence allows an attacker to maintain access beyond the current interaction.Fix: Remove any persistence mechanisms (cron jobs, startup scripts, state files). Skills should not maintain state across sessions without explicit user consent.
- medium Tool Misuse · line 177 Tool defaults are unsafe or overly permissive (e.g. disabled TLS verification, no authentication, world-writable permissions). Unsafe defaults widen the attack surface.Fix: Override unsafe defaults with secure settings (verify=True, auth required, restrictive permissions). Review and harden all tool configurations.
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 | $0.00107 | $0.03498 |
| Opus 5 | $0.00053 | $0.01749 |
| Sonnet 5 | $0.00021 | $0.00700 |
| Haiku 4.5 | $0.00011 | $0.00350 |
Grade A, and why
armada-pipeline scanned grade A with 1 finding 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.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
curl -s -X POST "https://authentik.nrp-nautilus.io/application/o/device/" \ How it starts
The opening of the file, as written. The whole thing — 292 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Armada Pipeline (NRP)
Why Armada: microslicing, not requeueing
Armada's value is not automatic retry — the NRP docs state plainly that "preempted jobs will not be automatically rescheduled". Reaching for Armada to survive preemption is the wrong reason.
The real reason is that Armada is not bound by the k8s indexed-Job completion cap (~200, an etcd pressure limit). Millions of completions are fine. That makes microslicing practical, and microslicing improves four things at once:
| few large jobs | many small slices | |
|---|---|---|
| unit of loss on preemption | hours | minutes |
| RAM requested | sized for the worst step in the chain | what each step actually needs |
| scheduling | needs large contiguous free slots; pods sit Pending |
fits in scraps almost anywhere |
| stragglers | one holds up the batch and can leave stale output | retries invisibly |
The scheduling point is the one most easily missed: 20 pods at 64Gi need ~1.3 TB free in large contiguous chunks, so realized parallelism is far below requested. Thousands of 8-16Gi slices pack into whatever is free and start immediately. Placing 10,000 small slices is often faster than placing 100 big ones — more so under preemption.
Big jobs also make you conservative: a 35-step chain must request the peak requirement of its worst step, so every step pays that cost. One unit per job asks for what it needs.
⛔ Authentication: use the device-code flow, not the documented PKCE flow
The config NRP publishes at https://nrp.ai/.armadactl.yaml uses PKCE (openIdAuth), which
binds 127.0.0.1:50000 and waits for a browser redirect. This cannot complete in a headless
shell. It hangs silently, prints no URL, and — critically — keeps holding port 50000, so
every later attempt dies with:
panic: listen tcp 127.0.0.1:50000: bind: address already in use
That panic is a symptom of the first hung process, not a separate fault. Kill the original before retrying.
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 First seen · 292 lines · 107 tokens per session scan A 628b90075601
armada-pipeline is a skill published in the GitHub repository boettiger-lab/data-workflows (5 stars, last pushed 2d ago), licensed BSD-3-Clause. It adds 107 tokens to every session and 3,498 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
Other skills, from other repositories
latchbio-integration
Build, register, debug, and operate bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake, programmatic execution, and Latch MCP. Use when authoring or deploying Latch workflows, configuring resources or interfaces, moving data, integrating Registry, or launching and…
modal-compute
Run explicitly chosen research benchmark or replication jobs on Modal's serverless infrastructure. Use when a Feynman research workflow needs burst remote GPU compute and the Modal CLI is available.
remote-compute-ssh
Evaluate and use SSH Remote Compute before choosing where to run GPU, high-memory, parallel, batch, model-inference, bioinformatics, or other long-running scientific work; supports short remote commands and asynchronous jobs with automatic harvest and analysis.
dnanexus-integration
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
latchbio-integration
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
modal-serverless-gpu
Run approved CPU or GPU work through OpenScience computejob on the user's configured Modal account. Use for isolated scientific scripts, dependency provisioning, durable outputs, logs, status, cancellation, and recovery. Never invoke the Modal SDK or CLI directly.