Merge pull request #231 from teharrison/master

validate metadata: now try both .xlsx and .xls before quitting (user may lie)
Edits to only update stage info if stages have progressed.  This prevents user confusion when a job is restarted.
Merge pull request #232 from jaredbischof/master

Edits to only update stage info if stages have progressed.  This prevent...
Necessary error-checking
Merge pull request #233 from jaredbischof/master

Necessary error-checking
dynamic_trim is not an option for filter_sequences.
if input file is empty, generate empty output file.
Merge pull request #234 from jaredbischof/master

Bug fixes for awe_preprocess_qc.pl
Fixed AWE state to check for after job submission.
Merge branch 'master' of github.com:MG-RAST/pipeline
Merge pull request #235 from jaredbischof/master

Fixed AWE state to check for after job submission.
Bug fix.
Merge pull request #236 from jaredbischof/master

Bug fix.
Removed reference to old AWE directory that no longer exists.
Merge pull request #237 from jaredbischof/master

Removed reference to old AWE directory that no longer exists.
Added exception to handle case when done stage has been run previously but not to completion.
Merge pull request #238 from jaredbischof/master

Added exception to handle case when done stage has been run previously b...
Updated to newer version of fastq-join which appears to handle more file formats.
Checking if sims.stats files exist rather than checking for zero or non-zero size.  Tested and works.
Merge pull request #239 from jaredbischof/master

Updated to newer version of fastq-join.