--reference and --protospacer not working

[mirpedrol]

          Hi there, appreciate these changes as this is my exact use case, but I've found that I'm getting errors when I specify both options in v2.1.1.

I have tried multiple combinations of specifying protospacer and reference in samplesheet and params (running via nextflow tower on aws batch) - the only way that leads to successful pipeline completion is with both specified only in the samplesheet.

When I use only --protospacer I encounter an error on CRISPRSEQ_PLOTTER where the protospacer is passed as [].

When I use --reference as a path to a .fasta I encounter an error on ORIENT_REFERENCE:

Caused by:
  No such variable: id -- Check script '.nextflow/assets/nf-core/crisprseq/./workflows/../modules/local/orient_reference.nf' at line: 2

Appreciate any help you may have!

Originally posted by @benemead in #43 (comment)