Closed snsansom closed 1 year ago
This pull request replaces pipeline_cellranger_multi.py with pipeline_cellranger.py.
The new pipeline:
See the docs in pipeline_cellranger.py for a description of the required inputs.
It is important to allocate the cellranger jobs 8 cores and at least 64GB of memory (in the yaml file). Recommend to use 128GB memory whenever possible. Cellranger runs dramatically slower with less memory, see the plots here: https://support.10xgenomics.com/single-cell-gene-expression/software/overview/system-requirements.
With 8 cores and 128GB the individual cellranger jobs complete in ~2 hours on the BMRC cluster.
This pull request replaces pipeline_cellranger_multi.py with pipeline_cellranger.py.
The new pipeline:
See the docs in pipeline_cellranger.py for a description of the required inputs.
It is important to allocate the cellranger jobs 8 cores and at least 64GB of memory (in the yaml file). Recommend to use 128GB memory whenever possible. Cellranger runs dramatically slower with less memory, see the plots here: https://support.10xgenomics.com/single-cell-gene-expression/software/overview/system-requirements.
With 8 cores and 128GB the individual cellranger jobs complete in ~2 hours on the BMRC cluster.