Merge pull request #211 from wtangiit/master

minor fix: match argument with the mgrast job template
Merge pull request #212 from wtangiit/master

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

Merging qc and preprocess stages into one.
New description and script name for merged stages.
Merge pull request #214 from jaredbischof/master

New description and script name for merged stages.
fix awe_preprocess to handle skip option and deal with fastq options
Merge pull request #215 from teharrison/master

fix awe_preprocess to handle skip option and deal with fastq options
Editing awe template to perform variable substitution to replace shock urls for certain files.
Editing awe template to perform variable substitution to replace shock urls for certain files.
Edited awe submission script to substitute in shock urls for certain files and default to no screening of input data unless it's defined.
Merge pull request #216 from jaredbischof/master

Editing awe submission script and workflow templates.
Rather than creating a template without screening, using the -skip option.
Rather than creating a template without screening, using the -skip option.
Merge pull request #217 from jaredbischof/master

 Rather than creating a template without screening, using the -skip option.
Bug fixes in creating valid AWE workflow document.
Merge pull request #218 from jaredbischof/master

Bug fixes in creating valid AWE workflow document.
Fixing Shock url for index file download.
Merge pull request #219 from jaredbischof/master

Fixing Shock url for index file download.
Fixing stage_id to match rna or dna clustering.