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maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
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bamCoverage memory in scRNAseq #284

Closed dpryan79 closed 5 years ago

dpryan79 commented 5 years ago

This is still using 8GB of RAM, when we need to reserve more (likely 20GB)

dpryan79 commented 5 years ago

shared/cluster.yaml can be updated to:

bamCoverage:
    memory: 4G
bamCoverage_RPKM:
    memory: 4G
bamCoverage_coverage:
    memory: 4G
bamCoverage_raw:
    memory: 4G
dpryan79 commented 5 years ago

sc_bam_featureCounts_genomic needs 2G

dpryan79 commented 5 years ago

Also, star_options needs to be added to the scRNA-seq yaml file and an equivalent option added to the CLI if it isn't already there. The internals file then has to be changed to respect this!

dpryan79 commented 5 years ago

sambamba in bioconda needs to be pinned to an ldc version.

dpryan79 commented 5 years ago

combine_sample_counts needs 4G in scRNAseq

dpryan79 commented 5 years ago

MACS2 in ChIP-seq and ATAC-seq needs 2G for some datasets.

dpryan79 commented 5 years ago

The bwamethIndex rule also needs more RAM (20G would suffice).