Add module loading to setup.sh & generated script
Add module loading for bwa and fastq scripts

Alternatively, these could be stored in create_processing.py, and added
to the generated scripts the same way that sample/flowcell info is.

Pros:
- Single place for all dependency information
- Can store them more compactly
- Could possibly add... idk, reporting features or something.

Cons:
- Disconnected from actual process steps
- Extra python code
- Updating required modules is slightly harder to remember to do
Describe $MODULELOAD in Readme
Fix bcl2fastq directory issue
Merge pull request #8 from fwip/load_modules

Load modules in scripts, instead of ahead-of-time. In the future we might want to only load modules if MODULELOAD is set!
Allow custom scripts and by project processing
Merge pull request #9 from StamLab/customprocessing

Allow custom scripts and by project processing
Add threads awareness to BWA alignment
Merge branch 'master' of github.com:StamLab/stampipes