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LCR-BCCRC / lcr-modules

Collection of standard analytical pipelines for genomic and transcriptomic data
https://lcr-modules.rtfd.io
MIT License
15 stars 7 forks source link

Specifying a Snakemake scheduler #161

Open lkhilton opened 3 years ago

lkhilton commented 3 years ago

Since adding the ILP scheduler, which is default as of Snakemake 5.26.1, I have a ton of issues with workflows with a large number of checkpoints. There are a number of GitHub issues related to this on the Snakemake GitHub page, but it hasn't been fixed yet. An easy workaround is to specify "--scheduler greedy" whenever launching Snakemake, which reverts to the original scheduling algorithm. It's easy enough to add this to the GAMBL wrappers, but is there a way to add this requirement to the dependency checking section at the top of each Snakefile so that other users don't struggle with this issue?

rdmorin commented 3 years ago

Seems reasonable. Does the setting get stored in the config?

lkhilton commented 3 years ago

Not that I know of, hence I'm not sure how easy it would be to implement.

rdmorin commented 3 years ago

Have we ruled out bundling the wrappers with LCR-modules and adding some more for other schedulers? Are they too tailored to our setup?

Lakshay-sethi commented 3 years ago

https://github.com/LCR-BCCRC/lcr-modules/blob/oncopipe-patch/oncopipe/setup.py