Limited CWL support

[LourensVeen]

There is currently no support for:

• secondaryFiles
• contents field (semantics of locations vs. path vs. contents is murky...)

[LourensVeen]

Also, there's no support for basename. According to the spec, if you give a location and a basename, the file should be downloaded from location and saved as basename. We currently ignore basename, and create a unique identifier ourselves.

It will probably still work however, since we pass the original input binding with only a modified location to cwltool, which should then do the rename.

[LourensVeen]

After careful study of the spec, and consideration of the fact that it's just an attempt at codifying the behaviour of cwltool, it seems that one should normally specify only location and perhaps basename if that is required. The implementation will then generate path for use with scripts inside the CWL. Alternatively, you can pass only contents, and cwltool will make it look like those were downloaded from somewhere. Specifying only path may or may not work; if it does it gets the file from the local file system. You're better off using a file:/// location then however.

[LourensVeen]

Also we're currently not supporting Directory inputs, which should be fairly simple, as it's just like staging a File, except you do a recursive copy.

[LourensVeen]

secondaryFiles now works, and basename does as well, so it's just Directory now.

[LourensVeen]

Which is actually issue #46, so closing this one.