pipeline_template

A template repository for pipeline code. For an example, see https://github.com/IGVF-UCSD/celloracle_pipeline/tree/dev. This should include:

README.md (this file)

• With details on the method

bin

• Compiled code that runs different iterations of each pipeline

pipeline_1

• Maybe this is the simple one sample one run pipeline

pipeline_2

• Maybe this is a SLURM pipeline

...

data

• Any auxiliary data needed for running methods
  • If it’s small, put it in the repo
  • If it’s large, link to it a file

env

• .def file for singularity set-up so you can run (recommended for reproducbility)
• .yaml file for conda set-up so you can run (recommended for modifcation)