Skip to content
This repository has been archived by the owner on Dec 19, 2023. It is now read-only.
/ bedmaker Public archive

pipeline to convert bigWig, bedGraph and other file types into BED format

Notifications You must be signed in to change notification settings

databio/bedmaker

Repository files navigation

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

About

pipeline to convert bigWig, bedGraph and other file types into BED format

Resources

Stars

Watchers

Forks

Packages

No packages published

Languages