protocol and seq_type are different

[davidrajones]

Add a warning that -*-protocol options and seq_type differ (at least for tumour). To ensure seqtype WXS doesn't get WGS as SAMPLE protocol set in the VCF.

[mcast]

Am I right in thinking there are two sets of label values?

• -seqType -st Sequencing type (pulldown|exome|genome|genomic|followup|targeted|rna_seq) - Passed to flagging
• -*-protocol -?p ... protocol [WGS|WXS|RNA|RNA-Seq|AMPLICON|TARGETED] (default WGS)

and so it'll be obvious to some folks which to use together, but not everybody.

Does the code translate? It's not obvious to me why -st can't be derived from the others, or how -np could usefully differ from -tp.