Geopts

Hi Phil, there's 2 main things in this PR, first a proper pre-runtime runfile parser for the memory / cores estimation in .cfmods, and a more sensible array of information passed to these from cf so they can make their decision on the memory request. An example of parsing them is in the example cfmod. Second, I added hardcoded genome paths for the STAR aligner and a .cfmod wrapper for that. I gather you're looking to get rid of hardcoded paths soon, but it works as a temporary measure.  I've only tested these on our cluster which can't use the shared memory options that STAR is capable of. Also fixed some bugs and added more control of trim_galore from the pipeline args.  I might add a sambamba wrapper later, but I think that's it from me for the time being, it's got everything I wanted :)
Cheers, Stuart

If this is the only difference between samtools versions, could we possibly try to find the version dynamically? Could be a bit messy, but may be nice to improve portability?

```
$ samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.19-44428cd

Usage:   samtools <command> [options]

Command: view        SAM<->BAM conversion
         sort        sort alignment file
         [...]
```

So perhaps could pull that. Having said that, it could get quite messy in practice and might not be worth the effort. Just a thought :smile: