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BIDS integration into snakemake workflows

Project description

Documentation Status

Snakemake + BIDS

This package allows you to build BIDS Apps using Snakemake. It offers:

  • Flexible data grabbing with PyBIDS, configurable solely by config file entries

  • Helper function for creating BIDS paths inside Snakemake workflows/rules

  • Command-line invocation of snakemake workflows with BIDS App compliance

  • Configurable argument parsing specified using the Snakemake workflow config

  • Execution either as command-line BIDS apps or via snakemake executable

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