You're reading the documentation for a development version. For the latest released version, please have a look at stable (v1.3.0).

Welcome to fsl-pipe’s documentation!

Framework to build pipelines in a declarative manner based on FileTrees. fsl-pipe has the following features:

  • The directory tree containing the input, intermediate, and output files are defined separately from the pipeline code in the convenient file-tree format

  • The pipeline writer only defines the individual recipes in regular python code (e.g., how to convert file A into file B or file B into C), which fsl-pipe will stitch together into a complete pipeline.

  • Users can run part of the pipeline by defining which files they actually want to produce.

  • By default, the pipeline will skip any jobs for which the output files already exist.

  • Jobs can be run locally in sequence as normal python functions or in parallel by submitting to a cluster queue (using fsl_sub) or by using dask.

Install using

pip install fsl-pipe

Typical usage:

from fsl_pipe import pipe, In, Out, Ref, Var

@pipe
def job(input_file: In, output_file: Out):
    # code to convert `input_file` to `output_file`

pipe.cli()  # runs command line interface

For the tutorial, select “Fsl-pipe tutorial” below. Other resources: