misleading documentation for report parameters

[fruce-ki]

-r is documented as defaulting to 1. As of version 0.8.* this is no longer the case. The parameter can be omitted completely.

Omiting the parameter has new behaviour, compared to setting it to 1:

• Setting it to 1 (or other integer(s)) will designate the corresponding samples as reference samples. Barcodes will be named by order of decreasing abundance in the reference, and any barcodes seen in bottlenecked samples that are not seen in the reference will be removed from all the samples.

• Omitting it allows processing of batches that do not have a reference sample. Barcodes will be named based on their abundances in the first available sample, but no filtering will take place based on their presence/absence in that sample.

• Update report readme

• Update workflow readme

• Update workflow

[fruce-ki]

The workflow script needs to be updated too. It does not accommodate thee omission of the reference parameter.