BICF Cellranger mkfastq Analysis Workflow

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BICF Cellranger mkfastq Analysis Workflow is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illumina’s bcl2fastq). This pipeline, used by the Bioinformatics Core Facility at UT Southwestern, demultiplexes samples from 10x Genomics single-cell libraries into fastqs. FastQC is run on the results all reports are collated with the MultiQC tool. 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.