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 sc-velocity-prepgit 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/sc-velocity-prep)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/sc-velocity-prep"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/sc-velocity-prep/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/tiangzlab/omicsclaw/sc-velocity-prep"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/sc-velocity-prep.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 1 finding, 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 Rogue Agent · line 3 Skill modifies its own code, configuration, or behavior at runtime. Self-modification enables an agent to escalate privileges, disable safety constraints, or install persistent backdoors.Fix: Prevent the skill from modifying its own code, SKILL.md, or configuration files. Treat skill files as read-only at runtime.
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 | $0.00070 | $0.01956 |
| Opus 5 | $0.00035 | $0.00978 |
| Sonnet 5 | $0.00014 | $0.00391 |
| Haiku 4.5 | $0.00007 | $0.00196 |
Grade A, and why
sc-velocity-prep 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 — 142 lines — stays where its author put it; the contents beside it link to each section on GitHub.
sc-velocity-prep
When to use
The user has raw Cell Ranger output (BAM + barcodes), STARsolo output,
or paired FASTQs and needs an AnnData with layers["spliced"] /
layers["unspliced"] (and optional layers["ambiguous"]) before
running sc-velocity. Two backends:
velocyto(default) — runsvelocyto runagainst a Cell Ranger BAM using a GTF. Produces a.loomand reads it back into AnnData.starsolo— re-runs alignment from FASTQ via STARsolo with the Velocyto solo subworkflow, or loads existing STARsolo Velocyto output directly when detected.
--base-h5ad lets you merge the velocity layers into an
already-processed AnnData (preserves obs / obsm / clustering).
For velocity estimation itself use sc-velocity. For non-velocity
scRNA preprocessing use sc-preprocessing.
Inputs & Outputs
Inputs
- Input kinds:
file,directory - Modalities: scrna
- File types:
.loom,.fastq,.fq - FASTQ structure: valid first record;
pairedlayout - Directory layouts (any):
paired-fastq,cellranger-output,starsolo-velocity
Outputs
tables/Summary.csvtables/barcodes.tsvtables/cell_metadata.csvtables/features.tsvtables/genes.tsvtables/metrics_summary.csvtables/top_velocity_genes.csvtables/velocity_layer_summary.csvfigures/velocity_gene_balance.pngfigures/velocity_layer_fraction.pngfigures/velocity_layer_summary.pngfigures/velocity_top_genes_stacked.png3M-february-2018.txt737K-august-2016.txtAligned.sortedByCoord.out.bamanalysis_summary.txtmultiqc_report.htmlpossorted_genome_bam.bamprocessed.h5advelocity_input.h5adweb_summary.htmlreport.mdresult.json- Processed AnnData (
saves_h5ad) — addslayers:spliced,unspliced,ambiguous
Flow
- Resolve
--input(Cell Ranger dir / STARsolo dir / FASTQ /.loom). - For
velocyto: locate BAM + barcodes, validate--gtf(or auto-pick fromresources/singlecell/references/gtf/), runvelocyto run, load.loom. - For
starsolo: detect existing STARsolo Velocyto output and load directly, OR re-run STARsolo Velocyto with--reference+--chemistry+ auto-detected--whitelist. - Optionally merge layers into
--base-h5ad. - Compute layer totals (
tables/velocity_layer_summary.csv) and top-gene balance. - Save
processed.h5ad, tables, figures,report.md,result.json.
What ships with it
7 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.
- 6d ago First seen · 142 lines · 70 tokens per session scan A 0dc9a542af5d
sc-velocity-prep is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 70 tokens to every session and 1,956 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 2026-09-03.
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