Experiences with workflow managers implemented in Haskell (funflow, porcupine, bioshake, ?)

This page summarizes the projects mentioned and recommended in the original post on /r/haskell

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  • awesome-pipeline

    A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

    There are a billion of them out there (https://github.com/pditommaso/awesome-pipeline), so the decision which one to choose is not exactly easy. Most of my colleagues rely on Nextflow and Snakemake, so I should consider these, but before I start to learn an entirely new language I wanted to explore the Haskell ecosystem for possible solutions. Strong typing should in theory be a perfect match for a pipeline manager. And having this in Haskell would simplify replacing some of my R code with Haskell eventually.

  • funflow

    Functional workflows

    Funflow: https://github.com/tweag/funflow

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  • porcupine-core

    Express parametrable, composable and portable data pipelines (by YPares)

    Porcupine: https://github.com/tweag/porcupine

  • bioshake

    Bioinformatics pipelines with Haskell and Shake

    Bioshake: https://github.com/PapenfussLab/bioshake

  • bionix

    Functional highly reproducible bioinformatics pipelines

    I wasn't satisfied with this and wanted the software to be managed too, so we ended up working on BioNix (https://github.com/PapenfussLab/bionix) which does both pipeline execution and software management. This is nice because it makes everything extremely reproducible and removes a lot of the pain of dealing with setting up software etc at various HPC facilities. The down side is Nix isn't typed, so the typing aspect of bioshake was ported on the back of a ADT implementation in Nix, and at least for my work it has caught a fair few mistakes. Of course this isn't Haskell so it doesn't satisfy your criteria, just though it's worth a mention.

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NOTE: The number of mentions on this list indicates mentions on common posts plus user suggested alternatives. Hence, a higher number means a more popular project.

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