search

fpbarthel / GLASS

GLASS consortium
MIT License
37 stars 13 forks source link

Neoantigen snakemake modules #127

Closed fsvarn closed 5 years ago

fsvarn commented 5 years ago

Adding modules to the Snakefile

fpbarthel commented 5 years ago

i added sequenza last push

fpbarthel commented 5 years ago

BTW. For snakemake we need to consider a re-write of the wrapper (bin/snakemake-run.sh) and parent Snakemake script. The issue is that having many rules loaded significantly increases the time to build the DAG because it will perform checks on any related rules.

See my post here: https://bitbucket.org/snakemake/snakemake/issues/1122/snakemake-dag-creation-is-slow

Unfortunately it's not possible to dynamically load includes from the parent Snakemake because these variables do not persist to child jobs.

A work around could be to get rid of the parent Snakemake script, and instead have a master include script that is included in each module. Then, instead of loading a parent Snakemake script, load the individual modules by themselves, and from within load the master include. That approach minimizes the number of rules loaded.

To do this, the wrapper would need to be rewritten to determine which snakemake module to load.

fsvarn commented 5 years ago

We need to reconcile the VEP versions in the mutation calling workflow and the neoantigen workflow. The cache used for the VEP in the mutation calling workflow does not work with the VEP used in the neoantigen workflow, likely due to different versions being used in each workflow

fsvarn commented 5 years ago

All modules integrated and functional.