Make denoise_wrapper work again after using the fancy existing_filepaths option parser, which broke the code.
Use 'existing_filepaths' option in denoiser.py
Establish working dir and prefix earlier in __call__
updated comment
Correct documentation of --header_id_regex option to RTAX.
Correct documentation of --read_id_regex and --header_id_regex options to RTAX.
fixed suppress_submit_jobs being hard-coded to False. It now takes the value of opts.suppress_submit_jobs
added non list lookups
missed one lookup
Make split mode work with multiple sff.txt files coming from the existing_filepaths option
fix erroneous typo from last commit
Merge branch 'master' of github.com:qiime/qiime into fix_denoiser_sff_file_lists
Pass list of files instead of file to fast_denoiser() in test
Merge pull request #1084 from audy/fix-supress-submit-jobs

fixed suppress_submit_jobs being hard-coded to False. It now takes the v...
Merge pull request #1056 from wasade/parallel_wrapper_tweaks

Establish working dir and prefix earlier in __call__
Merge pull request #1080 from davidsoergel/master

Correct documentation of --read_id_regex and --header_id_regex options to RTAX.
Merge pull request #1088 from wasade/issue_1087

added non list lookups
Update QIIME biom-format docs

Fixed some typos and updated to use ```biom convert``` command.
Update 18S tutorial to use ```biom convert```
Update shotgun tutorial to use ```biom convert```