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sciflow's Introduction

Scientific workflow management system

SciFlow is a DSL for building type-safe computational workflows. SciFlow is implemented based on the Free Arrow and is heavily inspired by the funflow package. The differences between SciFlow and funflow are:

  1. SciFlow uses Template Haskell to ease the process of workflow specification and to allow composition and reuse of defined workflows.

  2. SciFlow supports distributed computing thanks to Cloud Haskell!

Design

Features

  1. Easy to use and safe: Provide a simple and flexible way to design type safe computational pipelines in Haskell.

  2. Automatic Checkpointing: The states of intermediate steps are automatically logged, allowing easy restart upon failures.

  3. Parallelism and distributed computing support.

Examples

See examples in the "examples" directory for more details.

Featured applications

Here are some bioinformatics pipelines built with SciFlow.

sciflow's People

Contributors

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Stargazers

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Watchers

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Forkers

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sciflow's Issues

`runParser` conflict

runParser conflict:

Ambiguous occurrence ‘runParser’
    It could refer to either ‘Options.Applicative.runParser’,
    imported from ‘Options.Applicative’ at src/Scientific/Workflow/Main/Options.hs:9:1-36
    (and originally defined in ‘Options.Applicative.Common’)
  or ‘Scientific.Workflow.Main.Options.runParser’,
    defined at src/Scientific/Workflow/Main/Options.hs:58:1

Provide multiple data store backends

Sqlite is OK for storing small data. The rationale of using sqlite is that the states of computation steps are going to be small, but this may not be true for everyone. Sometimes it would be convenient to just store some huge intermediate results in the states rather than to create some temp files. For large binary data, using file system as the data store may be a better approach.

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