Main unstable

[rmcolq]

Closes a number of small outstanding issues.

1. Adds a script to check the input file where a single fastq file is provided, so that it can warn if there are duplicate headers. This was seen in some example data and would cause big problems for the viral reclassification step when run, as read names need to be unique. If it finds duplicate/unexpectedly interleaved files, tries to correct them but then exists. The user can try rerunning with the fixed files. I considered silently handling but this approach seemed dangerous.
2. Add messaging if paired reads provided and --paired not.
3. Add a workflow to run modules (it didn't work to add projectDir to script path as this is within the modules directory when a module is run). Also remove workflow definitions from these modules
4. Add total_len for input and output files
5. Add a warning for incorrect Phred parsing as this is thought to be a resolved issue