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Archived: This pipeline is now maintained as part of https://github.com/databio/bedboss

bedmaker

Pypiper pipeline to convert supported file types* into BED format and bigBed format

Before running the pipeline:

Users will need to format metadata as a Portable Encapsulated Project (PEP). Looper will use the PEP yaml config file to run the pipeline on all the dataset samples.

Validate the PEP with eido

The input PEP can be validated against the JSON schema in this repository. This ensures the PEP consists of all required attributes to run bedmaker pipeline.

eido -p <path/to/pep> -s pep_schema.yaml

To run the pipeline:

  1. Activate bulker environment
bulker load databio/bedmaker:default
bulker-activate databio/bedmaker:default
  1. Submit the pipeline with looper
looper run example/cfg.yaml

Currently supported formats*:

  • bedGraph
  • bigBed
  • bigWig
  • wig