Snakemake

[pommevilla]

Convert to a Snakemake pipeline. There should be a rules/mfp<step> file for each of the commands that currently exist in the pipeline.

User stories

• As a user, I want to be able to choose to run this on my local computer and not have to use Slurm
• As a user, I want to be able to choose between running the whole pipeline and running individual steps

Questions

• What are the targets?
• What are the inputs?
• What are the intermediate files?
• How can we make it so the user can run just part of the pipeline at a time?
  • Perhaps sending the commands to a Docker container which runs the desired step?