About the Bowtie2 index files, there are 3 options in the Agave app:

1. keep an unique field with maxCardinality=-1, when the user can upload the archive of the index, or all the files that make the index. Than change the wrapper so that it checks:
   • if the file uploaded is an archive (with file --mime-type), if so, unzip it
   • that all the required files are there ( .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2) [.fa is optional], if not exit with code 1 and report error
     This would prevent at the very first step (job submission) to go through if nothing is given.
2. Have two mutually exclusive fields (this can only be checked in the wrapper, so after the job was submitted and scheduled): one for archive submission, maxCardinality=1, and one for submission of index files, maxCardinality=-1. As per previous step check all the required files are given in the wrapper.
3. give multiple fields, one for each file. Archive field is mutually exclusive with all the others, that are mutually inclusive (this has to be in the wrapper). Each field has maxCardinality=1. This is similar to point 2, but:
   • user would potentially have less probability to forget some files (?)
   • this would work in the DE, as long as it doesn't support multiple file submission
   • i personally think is messier

fix the wrapper so that the tests don't fail