A Python DSL for bioinformatics pipelines

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  • License: Apache Software License
  • Author: Maxime Lévesque
  • Requires: Python >=3.7.7
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Project description

A Python DSL for pipelines

Don't Repeat Yourself (D.R.Y) while writing pipelines, and stay away from leaky abstractions, use DryPipe !

What is a pipeline ?

A pipeline could be described as "a bunch of programs feeding data to one another".

Programs within a pipeline tend to:

  1. run for a long time
  2. need large amounts of resources (cpu, memory, disk space, etc), requiring clusters to run (Slurm, Torque,etc)
  3. be written in different languaged, have different CLI interfaces, file formats, etc.
  4. long CODE->RUN->DEBUG->CODE cycles

The length of the development cycle makes pipelines difficult to debug.

https://drypipe.readthedocs.io/

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  • License: Apache Software License
  • Author: Maxime Lévesque
  • Requires: Python >=3.7.7
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