Re-upgrading CWL files

[golharam]

When I run cwl-upgrade on a set of CommandLineTools that I have in a directory, I can upgrade them one at a time and test they are okay.

I then have my workflows 1 directory above and upgrade them one at a time. During this process, the individual tools in the tools folder get upgraded/rewritten to the current working directory instead of the directory they were read from. Two things about this:

1. Since the tools were already upgraded, I don't think they need to be rewritten to the current working directory. That pollutes the filesystem.
2. The tools that do need to be upgraded should be rewritten to the directory they were read from.

Is it possible to provide options for both of the above, namely,

1. Only upgrade the cwl provided as input, and not dependent cwl files
2. Write upgraded CWL files to the same directory where they were read from; and instead of overwriting the existing CWL file, give it a new name or output to STDOUT.

[tetron]

So if I understand what you're saying:

1. Upgrading files are already at the latest version is redundant and should be skipped
2. The behavior of recursively updating files is surprising

If it creates the upgraded files in the same directory without updating references, the workflow won't actually refer to the upgraded tools.

I agree it should either only upgrade one file at a time, or it should write the new files to the same relative path as the original file (and moving the original file out of the way to a backup).