How to run kneaddata on all samples in an input directory?

Is there any way of having kneaddata run on all samples in an input directory (e.g., like metaphlan2) instead of running it for each sample separately? Additionally, can kneaddata automatically identify whether we have single-end vs. paired-end input files, e.g., by using a pair identifier similar to biobakery_workflows (’.R1’ and ‘.R2’)?

Hello, Kneaddata only runs on a single set of input files for a single sample. You could use the biobakery workflows to run kneaddata through a set of input files and also like you had mentioned to determine single-end vs paired-end.

Thank you,