kraken into QC-summary for rnaseq pipeline

quite a big pull request, so please take a look if it makes sense. 

I just added to RNAseq pipeline, for now. Easy to add to the others, but maybe better to start with this. Add some metrics to the project-summary as well. % of detected reads in the kraken database, and link to the summary file.

I try to change the minimum as possible and reuse code. Some re-arrangement in QC-summary, so Rory, if you can look at it carefully, better. 

let me know if I miss something.

test for rnaseq is working, and when I run my particular test with `kraken : true` is working as well.

Right now need to set up `kraken_db` to use the database that the user has to have somewhere, but planning to add the database to be installed with bcbio soon. 

don't know if you want to wait until I change that as well, I thought that that was too many changes.

Probably I will do a pull request to cloudBioLinux to add kraken to be installed with the other tools as well.

This also has a merge issue, since we just checked in the `startswith` fixes here. Could we skip the `has_aligned_reads` part and just run QC. It's going to be extremely rare something has zero aligned reads here and not sure it's going to blow anything up.