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/viral-ngs/regression-testingnpx skills add broadinstitute/viral-ngs --skill regression-testinggit clone --depth 1 https://github.com/broadinstitute/viral-ngsWhat 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 | $0.00000 | $0.01531 |
| Opus 5 | $0.00000 | $0.00766 |
| Sonnet 5 | $0.00000 | $0.00306 |
| Haiku 4.5 | $0.00000 | $0.00153 |
Grade A, and why
regression-testing 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 yesterday.
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 — 168 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Assembly Regression Testing
End-to-end regression testing for assembly pipeline changes against Terra submissions.
When to Use
Use this playbook when a PR makes functional changes to the assembly or variant-calling pipeline (e.g., swapping variant callers, changing alignment parameters, modifying consensus logic). It compares assembly outputs from old vs new code across hundreds of real samples to validate equivalence or improvement.
Prerequisites
- gcloud CLI -- authenticated with access to Terra workspace GCS buckets
- mafft -- for pairwise sequence alignment
- Python with pandas and matplotlib (e.g., a dataviz venv)
- dsub -- for running VADR batch jobs on GCP (see the
dsub-batch-jobsskill)
Workflow
Step 1: Set Up Terra Submissions (Manual)
The user must manually launch Terra submissions with old and new code:
- Run the pipeline on a representative dataset using the main branch Docker image
- Run the same pipeline on the same dataset using the feature branch Docker image
- Note the submission IDs and workspace bucket for both runs
Step 2: Discover Paired Samples
Use discover_pairs.py to find all comparable old/new sample pairs by crawling
GCS Cromwell output directories.
python discover_pairs.py \
--bucket <workspace-bucket-id> \
--old-sub <old-submission-id> \
--new-sub <new-submission-id> \
--output pairs.json
This produces a JSON mapping sample_name -> {old_tsv, new_tsv} for all samples present in both submissions.
Step 3: Compare Assembly Outputs
Use compare_sample_pair.py to compare each sample pair. This script:
- Downloads assembly_stats TSVs from GCS
- Compares metrics (coverage, % reference covered, length, etc.)
- Downloads FASTA assemblies and aligns them with mafft
- Reports SNPs, indels (events and bp), ambiguity diffs, and terminal extensions
python compare_sample_pair.py \
--old-tsv <gcs_uri> --new-tsv <gcs_uri> \
--work-dir ./results/<sample> \
--output-json ./results/<sample>.json
What ships with it
4 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
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.
- yesterday First seen · 168 lines · 0 tokens per session scan A 7765a57f7a7c
regression-testing is a skill published in the GitHub repository broadinstitute/viral-ngs (197 stars, last pushed 24d ago), licensed MIT. It costs nothing until one of its globs matches a file; then it loads 1,531 tokens. 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 2026-08-30.
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