testing

[KamilSJaron]

A list of check to be done in a test:

Input

• check that files on the input are correctly copied
• check that directories on the input are recursively copied
• check that parameters are ignores

Output

• check that there is no directory nesting when copying back output directory
• check that both individual files and wildcards are acceptable formats for output
• check that cleaning works if everything works fine

Environment

• check that failed execution do not delete any of the files
• check that conda activation works as expected (not sure what is expected conda #3)