Iontorrent support

[LordRust]

Since a few labs including the Swedish public health institute is using Iontorrent for sequencing, we need to support that.

• adding feature to parse the value "iontorrent" in the .csv input file (the "platform" field).
• optionally adding a field to the .csv file so that single ended (SE) illumina files are supported as well as PE
• modifying the processes that uses fastq files so they can work with SE data
• modifying parameters of de novo assemblers in order to optimize for the different error profile in iontorrent data. This is especially for SPAdes I think.

The error profile of Iontorrent data will likely give additional problems down the line, but these things should at least let us enable to analyse them.

[ryanjameskennedy]

As I understand it, the following modules are the only modules that need the option for SE/PE and/or platform:

• bwa
• kraken
• resfinder
• skesa
• spades
• virulencefinder