Merge pull request #1 from andrewjpage/master

Initial working script generation
Merge pull request #2 from andrewjpage/master

hard code paths to libraries
Merge pull request #3 from andrewjpage/master

dont allow duplicate study registrations
Merge pull request #4 from andrewjpage/master

cast as hash
Merge pull request #5 from andrewjpage/master

Update stampy default to pathogens version
Merge pull request #6 from andrewjpage/master

Add bowtie2 and stampy for all tasks
Merge pull request #7 from andrewjpage/master

Allow smalt parameters to be changed
Merge pull request #8 from andrewjpage/master

connection details
Merge pull request #9 from andrewjpage/master

make it harder to overwrite config files
Merge pull request #10 from andrewjpage/master

mapping config limits escaped out like all other pipelines
update warehouse host