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Nextflow to TOPP workflow conversion guide #304

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Nextflow to TOPP workflow conversion guide #304

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546545f
add manual conversion guide for Nextflow to TOPP workflow framework
claude Jan 14, 2026
15e34e0
add reference to Nextflow conversion guide in build_app docs
claude Jan 15, 2026
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10 changes: 10 additions & 0 deletions docs/build_app.md
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Expand Up @@ -66,3 +66,13 @@ Take a look at the example pages `Simple Workflow` or `Workflow with mzML files`
### Complex workflow using TOPP tools

This template app features a module in `src/workflow` that allows for complex and long workflows to be built very efficiently. Check out the `TOPP Workflow Framework` page for more information (on the *sidebar*).

### Converting Nextflow workflows

If you have an existing nf-core or Nextflow workflow that uses OpenMS TOPP tools (e.g., mhcquant, quantms), you can convert it to the TOPP Workflow Framework. See the [Nextflow Conversion Guide](nextflow_conversion_guide.md) for detailed instructions, including:

- Step-by-step conversion methodology
- Mapping Nextflow channels to FileManager operations
- Converting process definitions to `run_topp()` calls
- Handling parameters, conditionals, and file grouping
- Complete example conversions
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