This is an epic for completing the scATAC-seq in house pipeline that was started during the pipeline surge. This pipeline represents some key improvements to the SNAP-ATAC wrapped pipeline we implemented in Q2.
Where do I start?
The starting point for this work is the PR here that contains only the changes pertaining to this pipeline.
AC:
confirm mvp scientific validity of pipeline
Compare the output of this pipeline with the output of the snap-atac pipeline
Write tests for the pipeline
Incorporate the breaking out of the snap output into individual files (that will be done as part of finishing the snap-atac pipeline)
Document the inputs and outputs of the pipeline
Break up the main WDL to tasks
Fix the images and make new images that don’t overlap with the snap atac pipeline
Why/Background?
Where do I start?
AC:
┆Issue is synchronized with this Jira Epic