# Sdrf:convert

> Use when the user wants to choose an analysis pipeline, check SDRF compatibility with a pipeline, or understand how to go from SDRF to analysis.

- **Type:** Skill
- **Install:** `agentstack add skill-bigbio-sdrf-skills-sdrf-convert`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [bigbio](https://agentstack.voostack.com/s/bigbio)
- **Installs:** 0
- **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [bigbio](https://github.com/bigbio)
- **Source:** https://github.com/bigbio/sdrf-skills/tree/main/skills/sdrf-convert
- **Website:** https://sdrf.quantms.org

## Install

```sh
agentstack add skill-bigbio-sdrf-skills-sdrf-convert
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# 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

```text
Is it DIA data?
├── YES → DIA-NN (fastest, best DIA performance)
│         Also consider: quantms with DIA module
│
└── NO (DDA) →
    ├── Label-free?
    │   ├── Small 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:

1. **Label type**: DIA-NN doesn't support TMT (except PlexDIA). MaxQuant supports all.
2. **File format**: Check if raw files are compatible with the pipeline
3. **Modification support**: Some pipelines have limited PTM support
4. **Column completeness**: Each pipeline needs specific SDRF columns

## Conversion Commands

The `sdrf-pipelines` Python package provides the `parse_sdrf` CLI tool.
Install: `pip install sdrf-pipelines`

```bash
# For MaxQuant:
parse_sdrf convert-maxquant --sdrf file.sdrf.tsv --fastafilepath proteins.fasta

# For OpenMS:
parse_sdrf convert-openms --sdrf file.sdrf.tsv --onetable

# For DIA-NN:
parse_sdrf convert-diann --sdrf file.sdrf.tsv

# For MSstats (from OpenMS output):
parse_sdrf convert-msstats --sdrf file.sdrf.tsv --openswathtomsstats

# For NormalyzerDE:
parse_sdrf convert-normalyzerde --sdrf file.sdrf.tsv

# For quantms (Nextflow — reads SDRF directly, no conversion needed):
nextflow run bigbio/quantms --input file.sdrf.tsv --fasta proteins.fasta
```

Note: `quantms` reads SDRF natively via its own Nextflow modules. The SDRF is the
pipeline input — no `parse_sdrf` conversion step is needed.

## When the User Asks About a Specific Pipeline

1. Explain what the pipeline does and when to use it
2. Check if their SDRF is compatible
3. Show the conversion command
4. Explain what output files will be generated
5. Mention any limitations or common issues

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [bigbio](https://github.com/bigbio)
- **Source:** [bigbio/sdrf-skills](https://github.com/bigbio/sdrf-skills)
- **License:** MIT
- **Homepage:** https://sdrf.quantms.org

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-bigbio-sdrf-skills-sdrf-convert
- Seller: https://agentstack.voostack.com/s/bigbio
- Browse the marketplace: https://agentstack.voostack.com/browse

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Listed on AgentStack — the marketplace for AI agent skills and MCP servers. Every listing is security-reviewed. Creators keep 70%.