snakemake_10XG

Change the parameters in config.yaml file (data ID, reference path, threads, fastq directory, number ofe expected cells, chemistry and etc.)

No need to change Snakefile (it runs cellranger-2.2.0).

Use the following command line to run the pipeline:

nohup snakemake &

The processed data were saved in results_{dir}/; benchmark results were saved in benchmarks/