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 TianGzlab/OmicsClaw --skill bulkrna-read-alignmentgit clone --depth 1 https://github.com/TianGzlab/OmicsClawWrote 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/tiangzlab/omicsclaw/bulkrna-read-alignment)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/bulkrna-read-alignment"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/bulkrna-read-alignment.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 | $0.00064 | $0.00848 |
| Opus 5 | $0.00032 | $0.00424 |
| Sonnet 5 | $0.00013 | $0.00170 |
| Haiku 4.5 | $0.00006 | $0.00085 |
Grade A, and why
bulkrna-read-alignment 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 — 79 lines — stays where its author put it; the contents beside it link to each section on GitHub.
bulkrna-read-alignment
When to use
Run after the aligner / quantifier finishes, on the log file produced by
STAR (Log.final.out), HISAT2 (.log), or Salmon (meta_info.json).
Yields a one-page mapping-rate summary, strandedness inference, and a
gene-body coverage profile — the QC bridge between raw FASTQ and the
count matrix.
Inputs & Outputs
Inputs
- File types:
.out,.log,.json
Outputs
tables/alignment_stats.csvfigures/alignment_composition.pngfigures/gene_body_coverage.pngfigures/mapping_summary.pngreport.mdresult.json
Flow
- Auto-detect aligner from filename (
bulkrna_read_alignment.py:305-311):log.final.out→ STAR;meta_info→ Salmon; otherwise → HISAT2. - Parse the log into a numeric stats dict.
- Run quality assessment heuristics (high/medium/low mapping-rate buckets).
- Render figures and write
report.md+tables/alignment_stats.csv.
Gotchas
- Aligner detection is filename-based, not content-based.
bulkrna_read_alignment.py:305-311dispatches byinput_path.name.lower()— anything that is neitherlog.final.outnormeta_info(case-insensitive substring) is silently parsed as a HISAT2 log. A renamed STAR log will produce nonsense. Pass--method starexplicitly if your STAR file isn't named conventionally. - The skill consumes the LOG, not the BAM. Feeding a
.bamor.samfile as--inputwill not raise — the parser just finds zero matchable lines and reports an empty stats dict. Sanity-checkresult.json["summary"]["total_reads"]is non-zero before trusting any downstream summary. - Gene body coverage is synthetic in
--demomode (bulkrna_read_alignment.py:142-150). The 5'→3' bias profile in demo runs is a fixed reproducible curve, not derived from real input — useful for layout previews but not for assessing real RNA degradation.
What ships with it
5 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.
- 7d ago First seen · 79 lines · 64 tokens per session scan A 36707ad344e0
bulkrna-read-alignment is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 64 tokens to every session and 848 once invoked, about $0.0003 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 2026-08-30.
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