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 bigbio/sdrf-skills --skill sdrf-convertgit clone --depth 1 https://github.com/bigbio/sdrf-skillsWrote 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/bigbio/sdrf-skills/sdrf-convert)<a href="https://agentmods.dev/skills/bigbio/sdrf-skills/sdrf-convert"><img src="https://agentmods.dev/badge/skills/bigbio/sdrf-skills/sdrf-convert/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/bigbio/sdrf-skills/sdrf-convert"><img src="https://agentmods.dev/badge/skills/bigbio/sdrf-skills/sdrf-convert.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
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 | $0.00036 | $0.00989 |
| Opus 5 | $0.00018 | $0.00495 |
| Sonnet 5 | $0.00007 | $0.00198 |
| Haiku 4.5 | $0.00004 | $0.00099 |
Grade A, and why
sdrf-convert 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 — 101 lines — stays where its author put it; the contents beside it link to each section on GitHub.
SDRF Pipeline Guidance
You are helping the user choose and configure an analysis pipeline from their SDRF.
Supported Pipelines
sdrf-pipelines can convert SDRF to these formats:
| Pipeline | Command | Best For |
|---|---|---|
| OpenMS | convert-openms |
Flexible workflows, custom pipelines |
| MaxQuant | convert-maxquant |
DDA label-free, TMT, SILAC (desktop) |
| DIA-NN | convert-diann |
DIA/SWATH, PlexDIA (fast, scalable) |
| MSstats | convert-msstats |
Statistical analysis (downstream of search) |
| NormalyzerDE | convert-normalyzerde |
Normalization and differential expression |
| quantms | Nextflow pipeline | Cloud/HPC, complete workflow (uses SDRF natively) |
Pipeline Recommendation Logic
Is it targeted (PRM/SRM)? acquisition method = PRIDE:0000629 (PRM) / PRIDE:0000630 (SRM)
├── YES → Skyline / OpenSWATH (targeted) — not the DDA/DIA tree below
│
Is it DIA data? acquisition method = PRIDE:0000450 (incl. diaPASEF PRIDE:0000650, SWATH PRIDE:0000447)
├── YES → DIA-NN (fastest, best DIA performance)
│ Also consider: quantms with DIA module
│
└── NO (DDA) →
├── Label-free?
│ ├── Small study (<50 samples) → MaxQuant
│ ├── Large study (>50 samples) → quantms (scalable)
│ └── Custom workflow needed → OpenMS
│
├── TMT/iTRAQ?
│ ├── Standard TMT → MaxQuant or quantms
│ ├── TMT + phospho → MaxQuant (PTM scoring)
│ └── Large TMT cohort → quantms
│
└── SILAC?
└── MaxQuant (best SILAC support)
For statistical analysis (after search):
→ MSstats (gold standard for proteomics statistics)
→ NormalyzerDE (normalization comparison)
For cloud/HPC processing:
→ quantms (Nextflow, reads SDRF directly, no conversion needed)
Compatibility Checks
Before recommending, verify SDRF compatibility:
- Label type: DIA-NN doesn't support TMT (except PlexDIA). MaxQuant supports all.
- File format: Check if raw files are compatible with the pipeline
- Modification support: Some pipelines have limited PTM support
- Column completeness: Each pipeline needs specific SDRF columns
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 Changed 436e101e9300
- 10d ago First seen · 101 lines · 36 tokens per session scan A 1976dc98cb75
sdrf-convert is a skill published in the GitHub repository bigbio/sdrf-skills (18 stars, last pushed 4d ago), licensed MIT. It adds 36 tokens to every session and 989 once invoked, about $0.0002 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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