John Didion comments

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                                            John Didion

--nextseq-trim parameter settings

There is no default setting. If you specify `--nextseq-trim` you must specify the cutoff. You would want to determine the typical cutoff you'd use for trimming (i.e. if you were...

Should files imported from JSON be relative to the working directory or relative to the JSON file

The prohibition would be on using relative paths in path literals in WDL files. For your use case it would probably be better to allow the user to pass a...

Should files imported from JSON be relative to the working directory or relative to the JSON file

To answer the original question - I think the only thing that can work is for paths to be relative to the folder that contains the .json input file. This...

Disallow relative path literals in declaration expressions except in output section

I see the issue now. Yes it's true that defining a `File` variable in the `output` section has different semantics vs elsewhere. I would be in favor of disallowing relative...