Use Sample for targets
Update generic_target_generator to return correct sample_run_prefix
Make task-specific target generator handlers fall back on backend if called via pipeline module
Merge branch 'master' into develop
Add docs
Add docs
Update collect_sample_runs to only collect runs for a given sample
Add SphinxReport to script
Merge branch 'feature/project_summary' into develop
Merge branch 'develop'
Update config file
Update resyncMates to not hash entire sequence files but only the sequence ids
Merge branch 'develop'
Add new default to resyncMates; read files in parallel, assuming all ids are present
Merge branch 'develop'
Merge branch 'master' into feature/halomerge
Update config to deal with HaloPlexCombine. Fixes issue #2
Merge branch 'feature/halomerge' into develop