.gitignore
Only very light trimming before merging paired end reads.
This fixes the problem of almost all pairs not merged due to trimming.
Fixed indent
Get locations of dependencies from environment instead of hard-wired vars
Deleted files not used for 16S and having hardwired dependency paths.
If you ever need these files, pull them from history and edit
the dependency paths.
Replaced more hardwired dependency paths with env vars.
Calls to this code will currently fail because we do not define
these env vars. It seems that this code is never called for 16S.
Instead of hard-wired, pull --annotations default from YAP_DATA env var
Propagating environment to batch jobs and batch jobs of batch jobs
Reduced default number of cores per node and himem queue requirement.
Request RAM 2G per core and have option to turn on debugging of queue jobs
Fixed remaining tab replacement indentation bugs.
These appeared after tab replacement where space and tab were mixed
in original indentation.