Viash Hub

Name	Type & Properties	Description
--input	file required	Path of Illumina BCL run folder.
--csv	file required	The path to the simple layout sample sheet.
--lanes	string multiple	bcl2fastq option. Semicolon-delimited series of lanes to demultiplex. Use this if you have a sample sheet for an entire flow cell but only want to generate a few lanes for further 10x Genomics analysis.
--use_bases_mask	string multiple	bcl2fastq option. Use to clip extra bases off a read if you ran extra cycles for QC.
--delete_undetermined	boolean_true	bcl2fastq option. Delete the Undetermined FASTQs generated by bcl2fastq. Useful if you are demultiplexing a small number of samples from a large flow cell.
--barcode_mismatches	integer	bcl2fastq option. Use this option to change the number of allowed mismatches per index adapter (0, 1, 2).
--output	file required output	The folder to store the demux results
--reports	file output	Reports directory

demux/cellranger_atac_mkfastq