BICF Cellranger count Analysis Workflow

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BICF Cellranger count Analysis Workflow is a wrapper for the cellranger count tool from 10x Genomics. This pipeline, used by the Bioinformatics Core Facility at UT Southwestern, takes fastq files from 10x Genomics single-cell gene expression libraries and passes them to cellranger count, managing parallelization of multiple runs, as well as, aggregation as appropriate. This pipeline is primarily used with a SLURM cluster on BioHPC, but it should be able to run on any system that Nextflow supports. Additionally, this pipeline is designed to work using a simple web interface.