set seqkit sequencing type in configuration file

[vaofford]

When a fastq has a missing 1st entry (due to short reads and trimming) seqkit seq infers that the type of sequences in the file is "unlimit" rather than "dna": https://bioinf.shenwei.me/seqkit/usage/#seq

"unlimit" type sequences cannot be complemented and the files currently returned by --read_transform "reverse_complement" are just reversed. This will mean no reads match template libraries for quantification.

Specify -t dna or --seq-type dna will fix. This could limits quants from working with RNA sequences - is this a potential issue?

[vaofford]

Several ways we could tackle this:

1. code change to seq-kit module -> ideally avoid this so we keep the module generic and working for all sequencing types
2. update the seqkit module default commands in the configuration file (https://github.com/cancerit/QUANTS/blob/develop/conf/modules.config) -> would require a new release
3. add the seqkit_seq_options to the parameter JSON we supply at run time -> wouldn't require a new release

@jamieb63 does (3) work ok with a test set of data?