used software of your workflow
songxh1996 opened this issue · comments
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???
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!