used software of your workflow

[songxh1996]

Thanks for your contribution, I want to refer to your process to implement it step by step, but I can't find the detailed use method, software and workflow，such as smtools、bismark、or piard???

[paul-sud]

Hi there,

You might find some of these links useful. Here is a high level schematic of the pipeline:
https://www.encodeproject.org/pipelines/ENCPL182IUX/

The workflow is contained entirely in this file: https://github.com/ENCODE-DCC/wgbs-pipeline/blob/dev/wgbs-pipeline.wdl You can see how tasks are orchestrated in the workflow block and see the implementation of each task under their respective task blocks.

Lastly, the Dockerfile contains all the software dependencies and versions needed to run the pipeline:
https://github.com/ENCODE-DCC/wgbs-pipeline/blob/dev/Dockerfile . In this image we also install some Python packages from a couple requirements files: https://github.com/ENCODE-DCC/wgbs-pipeline/blob/dev/requirements.txt and https://github.com/ENCODE-DCC/wgbs-pipeline/blob/dev/requirements-gembs.txt

Hope that helps!