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 thesecondfox/skill --skill bio-workflows-edna-pipelinegit clone --depth 1 https://github.com/thesecondfox/skillWrote 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/thesecondfox/skill/bio-workflows-edna-pipeline)<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-workflows-edna-pipeline"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-workflows-edna-pipeline.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 | $0.00072 | $0.04333 |
| Opus 5 | $0.00036 | $0.02167 |
| Sonnet 5 | $0.00014 | $0.00867 |
| Haiku 4.5 | $0.00007 | $0.00433 |
Grade A, and why
bio-workflows-edna-pipeline 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 4d 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 — 422 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: DADA2 1.30+, FastQC 0.12+, MultiQC 1.21+, cutadapt 4.4+, phyloseq 1.46+, vegan 2.6+
Before using code patterns, verify installed versions match. If versions differ:
- R:
packageVersion('<pkg>')then?function_nameto verify parameters - CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
eDNA Metabarcoding Pipeline
"Process my eDNA samples from raw reads to community ecology" → Orchestrate primer removal, denoising (OBITools3 or DADA2), contamination filtering, taxonomy assignment, Hill number diversity estimation, and constrained ordination for species-environment analysis.
Complete workflow from raw amplicon sequences to community ecology analysis, supporting both OBITools3 and DADA2 processing paths.
Pipeline Overview
Raw amplicon FASTQ (demultiplexed)
|
v
[1. QC] ------------------> FastQC / MultiQC quality assessment
|
v
[2. Primer Removal] ------> Cutadapt (remove forward + reverse primers)
| |
| +---> QC: reads per sample >1000
|
+--- Path A: OBITools3 +--- Path B: DADA2
| | | |
| v | v
| [3a. obi alignpairedend] [3b. filterAndTrim]
| | | |
| v | v
| [4a. obi uniq] | [4b. learnErrors + dada]
| | | |
| v | v
| [5a. obi ecotag] | [5b. assignTaxonomy]
| |
+-------- Merge -----------+
|
v
[6. Contamination Filter] -> decontam / microDecon (negative control removal)
|
v
[7. Taxonomy Table] -------> Species x sample matrix
|
v
[8. Diversity Analysis] ---> iNEXT Hill numbers (q=0,1,2)
|
v
[9. Community Comparison] -> vegan CCA/RDA + indicspecies
|
v
Species table + diversity metrics + ordination plots
What ships with it
1 file 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.
- 4d ago First seen · 422 lines · 72 tokens per session scan A 44d2ae0fb804
bio-workflows-edna-pipeline is a skill published in the GitHub repository thesecondfox/skill (3 stars, last pushed 5mo ago), licensed MIT. It adds 72 tokens to every session and 4,333 once invoked, about $0.0004 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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