Merge pull request #202 from jaredbischof/master

ignoring all negative values here
fix variable name
Merge pull request #203 from teharrison/master

fix variable name
Merge pull request #204 from jaredbischof/master

Added shock parameter for overriding the Shock URL that the job results ...
Merge pull request #205 from jaredbischof/master

Added auth token for downloading jobs from Shock.
Merge pull request #206 from jaredbischof/master

Update to config variable name
Merge pull request #207 from jaredbischof/master

Fixing bug in md5 counts.
Merge pull request #208 from jaredbischof/master

Adding QC stage to MG-RAST AWE workflow
Merge pull request #209 from jaredbischof/master

Added download of qc stage output files to AWE workflow document.
Merge pull request #210 from jaredbischof/master

More updates to AWE template to make AWE server happy.
match argument with the awe template
Merge pull request #211 from wtangiit/master

minor fix: match argument with the mgrast job template
add awe_preprocess_qc.pl, a script merging preprocess and qc stages to reduce data movement
typo fix in awe_preprocess_qc.pl
Merge pull request #212 from wtangiit/master

merging preprocess and qc stages to reduce data movement
Merge pull request #213 from jaredbischof/master

Merging qc and preprocess stages into one.
New description and script name for merged stages.