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-multi-countgit 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-multi-count)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/sc-multi-count"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/sc-multi-count/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-multi-count"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/sc-multi-count.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 | $0.00066 | $0.01265 |
| Opus 5 | $0.00033 | $0.00633 |
| Sonnet 5 | $0.00013 | $0.00253 |
| Haiku 4.5 | $0.00007 | $0.00127 |
Grade A, and why
sc-multi-count 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 5d 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 — 115 lines — stays where its author put it; the contents beside it link to each section on GitHub.
sc-multi-count
When to use
The user has run sc-count (or another counting backend) on multiple
samples separately and now needs them merged into one AnnData with a
canonical sample-label column for downstream batch-aware analysis.
Replaces cellranger aggr for the OmicsClaw pipeline — preserves the
canonical AnnData contract instead of re-counting.
Inputs & Outputs
Inputs
- Modalities: scrna
Outputs
tables/Summary.csvtables/barcode_metrics.csvtables/barcodes.tsvtables/cell_metadata.csvtables/features.tsvtables/genes.tsvtables/metrics_summary.csvtables/per_sample_summary.csvfigures/barcode_rank.pngfigures/count_complexity_scatter.pngfigures/count_distributions.pngfigures/sample_composition.png3M-february-2018.txt737K-august-2016.txtAligned.sortedByCoord.out.bamanalysis_summary.txtmultiqc_report.htmlpossorted_genome_bam.bamprocessed.h5adstandardized_input.h5adweb_summary.htmlreport.mdresult.json- Processed AnnData (
saves_h5ad) — addsobs:sample_id
Flow
- Collect per-sample AnnData paths from each
--input <path>flag (action="append"); paired--sample-id <id>flags assign sample labels. - Load each, normalise the single-cell contract (
layers["counts"],adata.raw, gene name harmonisation). - Stack with explicit sample-label per cell.
- Write merged AnnData; emit per-sample / per-barcode summary tables.
- Render barcode-rank + composition figures.
- Emit
report.md+result.json.
Gotchas
--inputisaction="append"— repeat the flag, do not comma-split.sc_multi_count.py:315declares--inputwithaction="append". Pass--input s1.h5ad --input s2.h5ad --input s3.h5ad; a single comma-separated value (--input s1.h5ad,s2.h5ad) is treated as one literal path that does not exist and triggersFileNotFoundError. No directory expansion.- At least two
--inputpaths are required.sc_multi_count.py:335callsparser.error("At least two --input paths required when not using --demo.")if you pass zero or one. For a single-sample run you don't need this skill — just use the upstreamsc-countoutput directly. - Missing input file → hard fail.
sc_multi_count.py:346raisesFileNotFoundErrorwhen any individual--inputpath does not resolve. In batch pipelines, a single mistyped sample name aborts the whole merge — pre-flight your file list. --r-enhancedis accepted but produces no R plots. This skill emits Python figures only; the flag exists for CLI consistency.- No within-sample re-counting. This is a stitching skill — it stacks already-canonical AnnData objects. If a per-sample input has a non-canonical matrix layout, run
sc-standardize-inputon each before this; otherwise the merged contract may surface incoherent per-cell metrics downstream.
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.
- 5d ago First seen · 115 lines · 66 tokens per session scan A e8c59384c74c
sc-multi-count is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 66 tokens to every session and 1,265 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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