Allow users to specify loci parameters solely through the command line

[jackscanlan]

Default samplesheet could be included in ./assets, and the --lp_* parameters could be used to modify it.

Requirements:

• add parameters to set (and overwrite) the pcr_primers and target_gene fields in the loci_params sheet (probably use --pcr_primers and --target_gene parameters)
  • support for lists
• parse_inputs.R needs to use above parameters to edit the loci_params sheet (imported from default in ./assets) and then parse the replacement parameters
• change channel logic so default .csv is used if --loci_params is unset
• pipeline schema needs to be updated to allow --loci_params to be unset if --pcr_primers and --target_gene are set

Reason to do this is to eliminate requirement of creating a loci_params.csv in addition in to the samplesheet, for flexibility. But overall, .csv files probably preferred for complex experimental designs of three or more multiplexed loci, as lists of parameters get difficult

Note: single values passed to --lp_* overwrite all rows of the sheet, which is convenient for the parameters that are likely to be the same for all primers