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maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
MIT License
374 stars 85 forks source link

memory resources allelic mode #958

Closed WardDeb closed 7 months ago

WardDeb commented 8 months ago

The default (1G/thread) doesn't cut it for samples with 40 - 70M PE reads in allelic mode, causing cgroup failures or spillage to disk.

up memory defaults for sambamba_markdup, bamsort_allelic & snp_split