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# 🚀🧬 MrBiomics - Modules & Recipes augment Bioinformatics for Multi-Omics Analysis at Scale
# 🚀 MrBiomics 🧬
## <ins>M</ins>odules & <ins>R</ins>ecipes augment <ins>Bio</ins>informatics for Multi-<ins>Omics</ins> Analyses at <ins>S</ins>cale
> _"For many outcomes, roughly 80% of consequences come from 20% of causes (the "vital few")."_ - The Pareto Principle by Vilfredo Pareto
Get 80% of all standard (biomedical) data science analyses done semi-automated with 20% of the effort, by leveraging [Snakemake's](https://snakemake.github.io/) module functionality to use and combine pre-existing workflows into arbitrarily complex analyses.

> [!IMPORTANT]
> If you use **MR.PARETO**, please don't forget to give credit to the authors by citing this original repository and the respective **Modules** and **Recipes**.
> If you use **MrBiomics**, please don't forget to give credit to the authors by citing this original repository and the respective **Modules** and **Recipes**.
# ⏳ TL;DR - More Time for Science!
> _"Programming is about trying to make the future less painful. It’s about making things easier for our teammates."_ from _The Pragmatic Programmer_ by Andy Hunt & Dave Thomas
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> ⭐️ **Star and share modules you find valuable** 📤 — help others discover them, and guide our future work!
> [!TIP]
> For detailed instructions on the [installation](../../wiki/Installation), [configuration](../../wiki/Configuration), and [execution](../../wiki/Execution) of modules, you can check out the [wiki](https://github.com/epigen/mr.pareto/wiki). Generic instructions are also shown in the modules' respective [Snakmake workflow catalog entry](https://snakemake.github.io/snakemake-workflow-catalog).
> For detailed instructions on the [installation](../../wiki/Installation), [configuration](../../wiki/Configuration), and [execution](../../wiki/Execution) of modules, you can check out the [wiki](https://github.com/epigen/MrBiomics/wiki). Generic instructions are also shown in the modules' respective [Snakmake workflow catalog entry](https://snakemake.github.io/snakemake-workflow-catalog).
# 📋 Projects using multiple Modules
> _“Absorb what is useful. Discard what is not. Add what is uniquely your own.”_ - Bruce Lee
You can [(re-)use and combine pre-existing workflows](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#using-and-combining-pre-exising-workflows) within your projects by loading them as [**Modules**](https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#snakefiles-modules) since [Snakemake 6](https://slides.com/johanneskoester/snakemake-6#/8). The combination of multiple modules into projects that analyze multiple datasets represents the overarching vision and power of MR.PARETO.
You can [(re-)use and combine pre-existing workflows](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#using-and-combining-pre-exising-workflows) within your projects by loading them as [**Modules**](https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#snakefiles-modules) since [Snakemake 6](https://slides.com/johanneskoester/snakemake-6#/8). The combination of multiple modules into projects that analyze multiple datasets represents the overarching vision and power of **MrBiomics**.

> [!NOTE]
> When applied to multiple datasets within a project, each dataset should have its own result directory within the project directory.
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```

> [!TIP]
> A full [tutorial](../../wiki/Module-Usage-in-Projects) is available on the [wiki](https://github.com/epigen/mr.pareto/wiki).
> A full [tutorial](../../wiki/Module-Usage-in-Projects) is available on the [wiki](https://github.com/epigen/MrBiomics/wiki).

# 📜 Recipes
> _"Civilization advances by extending the number of important operations which we can perform without thinking of them."_ - Alfred North Whitehead, author of _Principia Mathematica_

**Recipes** are combinations of existing modules into end-to-end best practice analyses. They can be used as templates for standard analyses by leveraging existing modules, thereby enabling fast iterations and progression into the unknown. Every recipe is described and presented using a [wiki](https://github.com/epigen/mr.pareto/wiki) page by application to a public data set.
**Recipes** are combinations of existing modules into end-to-end best practice analyses. They can be used as templates for standard analyses by leveraging existing modules, thereby enabling fast iterations and progression into the unknown. Every recipe is described and presented using a [wiki](https://github.com/epigen/MrBiomics/wiki) page by application to a public data set.

> [!TIP]
> Process each dataset module by module. Check the results of each module to inform the configuration of the next module. This iterative method allows for quick initial completion, followed by refinement in subsequent iterations based on feedback from yourself or collaborators. Adjustments in later iterations are straightforward, requiring only changes to individual configurations or annotations. Ultimately you end up with a reproducible and readable end-to-end analysis for each dataset.
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> ⭐️ **Star this repository and share recipes you find valuable** 📤 — help others find them, and guide our future work!

# 📚 Resources
- [MR.PARETO Wiki for instructions & tutorials](https://github.com/epigen/mr.pareto/wiki)
- [GitHub list of MR.PARETO modules](https://github.com/stars/sreichl/lists/mr-pareto)
- [My Data Science Setup - A tutorial for developing Snakemake workflows and beyond](https://bit.ly/TAP-data-science-setup)
- [GitHub Page of this repository](https://epigen.github.io/mr.pareto/)
- [MrBiomics Wiki for instructions & tutorials](https://github.com/epigen/MrBiomics/wiki)
- [GitHub list of MrBiomics modules](https://github.com/stars/sreichl/lists/MrBiomics)
- [My Data Science Setup - A tutorial for developing Snakemake workflows and beyond](http://setup.polytechnist.me)
- [GitHub Page of this repository](https://epigen.github.io/MrBiomics/)
- Curated and published workflows that could be used as modules:
- [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/)
- [WorkflowHub](https://workflowhub.eu/)
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