Merge pull request #11 from mariogiov/devel

Convert from Sthlm --> Uppsala directory format as Piper expects

Great work Mario
Merge pull request #17 from mariogiov/devel

WIP clearly, start writing tests

The J.Doe thing can wait the next pull request
Merge pull request #18 from mariogiov/devel

Looks good
Merge pull request #19 from mariogiov/devel

Merging and going to try this out!!!
added extra error message  when a project that do not exists in the flowcell is specified
messed around with create_report_tsv(project): problem not solve Mario should look into it but for now it is not needed
convert_sthlm_to_uppsala now works --> Mario needs to check if I am using the same logic
build_setup_xml(project, config) works on test data. Unsure what happens when multiple flowcells are present and multiple samples.... we will see monday
tested on G.Gri... working need to fix probelms and allow re-runsgit add ngi_pipeline/piper_ngi/__init__.pygit add ngi_pipeline/piper_ngi/__init__.py
add dummy execution file to debug (ipython does not allow to make changes on the code and re-run, tried autoreload but had problem with nested includes
Merge pull request #22 from vezzi/devel

NGI_pipeline first working version
Merge pull request #3 from NationalGenomicsInfrastructure/devel

Debugging changes from vezzi
Fix up error messages in case of no projects found in flowcells
Change parameter order in conductor main function; change relative->absolute imports; update full pipeline testing script
Remove unnecessary import
Add various notes, modify symlinking/sthlm2UUSNP pieces a bit
Match indentation
Comment out code made redundant by sthlm2UUSNP (may need it later); search multiple locations for Piper global configuration file
Remove unneeded code
Remove yaml config loading; circular import and unneeded. Resolve at some point