New description and script name for merged stages.
Merge pull request #214 from jaredbischof/master

New description and script name for merged stages.
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.
Merge pull request #220 from jaredbischof/master

Fixing stage_id to match rna or dna clustering.
Fixing input/output filenames
Merge pull request #221 from jaredbischof/master

Fixing input/output filenames
Allowing bowtie screening to be skipped without an error.
Merge pull request #222 from jaredbischof/master

Allowing bowtie screening to be skipped without an error.