search

hpc-carpentry / old-hpc-workflows

Scaling studies on high-performance clusters using Snakemake workflows
https://www.hpc-carpentry.org/old-hpc-workflows/
Other
8 stars 2 forks source link

"Perfect" `snakemake` file for Amdahls Law #12

Open ocaisa opened 2 years ago

ocaisa commented 2 years ago

Ultimately the lesson ends up with the "perfect" Snakefile for the example it uses (which can be found in the .solutions/completing_the_pipeline folder of workflow-engines-lesson.zip). We need to get to a similar perfect Snakefile for own use case (hopefully one that uses all the material in the lesson). Once we have that we can work backwards to replace the existing example with our own.

ocaisa commented 2 years ago

Perfection in our case is not just the Snakemake file, it will need to include the profile for the cluster and whatever method we recommend to get the computing environment we require to run our tasks.