Pipe-tree: declative pipelines based on FileTrees

Framework to build pipelines in a declerative manner based on FileTrees. Pipe-tree has the following features:

• The directory tree containing the input, intermediate, and output files are defined separately from the pipeline 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 pipe-tree will stitch together into an acyclical graph

• Users can run part of the pipeline

• By default, the pipeline will not rerun 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.

Available resources:

• Gitlab repository: https://git.fmrib.ox.ac.uk/ndcn0236/pipe-tree
• Documentation: https://open.win.ox.ac.uk/pages/ndcn0236/pipe-tree/