I am attempting to automate a scRNA-seq workflow for 10x genomics data to be processed by cellranger.
As described in this link: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/fastq-input , fastQ files are made in several ways, and the folder structure in which the fastQs are delivered tells you a lot about the processing used to create the fastQs (e.g. bcl2fastq versus mkfastq).
Now then, because both this folder structure and the file naming conventions provide a substantial amount of info., it seems possible to set up the cellranger --count command correctly simply by parsing the input structure.
My question is, has anyone already done this? I would love to not have to rewrite this functionality. Thank you very much for your time.