fix cluster file parsing
Merge pull request #354 from teharrison/master

fix cluster file parsing
add rat to harcoded list
Merge pull request #355 from teharrison/master

add rat to harcoded list
Added options seem to fix mongo errors when talking to m5nr.
Unpacking database certificates as user that is running the command.  Also, not deleting these files after task completion for the time being.
Merge pull request #356 from jaredbischof/master

Added options seem to fix mongo errors when talking to m5nr.
Removed option that causes client failure to connect to mongodb.
Merge pull request #357 from jaredbischof/master

Removed option that causes client failure to connect to mongodb.
update to scripts for inbox actions
Merge branch 'master' of github.com:teharrison/pipeline
Merge branch 'master' of github.com:MG-RAST/pipeline
fix syntax errors
reduce default chunk size to process
Merge pull request #358 from teharrison/master

update to scripts for inbox actions
add format option to qc and preprocess stages incase sequence format not same as suffix, still backwards compatable
Merge branch 'master' of github.com:MG-RAST/pipeline
update usage
Merge pull request #359 from teharrison/master

add format option to qc and preprocess stages incase sequence format not same as suffix, still backwards compatable
fix fasta/fastq from being determined from file name