Management of Directories

[camilovelezr]

Moving PolusAI/image-tools#466 to correct repo

Summary

Management of directories by the WIC needs to be investigated.

What is the current bug behavior?

After initial investigation, it seems that any output directory hierarchy is ignored and output directory is created in the working directory.
Intermediary directories created by wic are also created directly created in the working directory. Their names are build from the named input preprended the step name (ex: inpDirOmeConverter). This means that running several workflows will eventually shove all data in the same directory.

What is the expected correct behavior?

• output paths hierarchy should not be ignored and the full path created. Relative paths will not work in certain configurations.
• intermediary directories (created when inputs and outputs are linked) should be created within a directory with WORKFLOW_NAME or a similar idea to help discriminate between various workflow outputs.