Object out of the loop

[ypar]

While cimr-d is handling cimr calls per file in the submitted/ directory, individual modules within cimr are set such that they can run independently. In the Yamler class, the file loops in convert_yaml is passing objects (y, genome_build, columnset) that are specific to a file (the last file to be specific) along with a fileset object. This will not work when Yamler class is called with a set of yaml files as inputs.

Quote from @dongbohu who reported this bug:

When yaml_files includes more than one file, I don't think this works, because y, genome_build and columnset are only values specified in the LAST yaml file. The tests didn't fail because they always call cimr command in this fashion:
cimr ... -yaml-file <single_file_name>

The bug can probably displayed when this module is run in the fashion of:
python yamler.py     # supported by lines 559-560
while submitted/ sub-dir includes multiple yaml files.

It does not affect cimr-d processing using cimr, but it does need to be addressed.

[ypar]

this has been resolved