Feature/Optional_Files

[geertvandeweyer]

As raised by Peter Thomas on slack :

Added support for optional files in the AWS handling of (de)localization and caching:

• support for "File?"
• support for "Array[File?] in manual assignment
• support for "Array[File?]" in globbing

Tested for input and output of individual tasks and workflows:

• optional files are allowed to be missing during (de)localization on both S3 and EFS (mentioned to log)
• optional files are considered valid in cache-hash calculation (if missing in original, and still missing => valid hit) (silent)

extra : minor optimization on hashing through EFS/MD5 files : if considered invalid, return a random string instead of the same message each time. This forces a cache-break.

Note: Mixed types are not supported and cast to mandatory files:

• an array of [File_1, File_2] where _1 is optional and _2 is not, will be "non-optional" completely.

For testing : see release 87.1-AWS in my own fork : https://github.com/geertvandeweyer/cromwell/releases/tag/87.1-AWS