Closed jmuhlich closed 6 months ago
Now that I think about it some more, it may actually be best to enforce that these paths are absolute to help with reproducibility and self-documentation of the resulting params.json.
I believe this stems from core nextflow path parsing, which nf-validation delegates to. nextflow.Nextflow.file()
will raise an exception if the path is a local file path that doesn't start with a /
. This is probably a good thing in the end, but nf-validation's use of that particular code path doesn't seem quite right since it does a lot of other things. (like glob expansion!)
Description of the bug
Specifying a param value like --input_cycle as a bare filename does not work -- nextflow doesn't seem to "see" the file. Prefixing the filename with its full absolute path works around this. This is probably something about nf-validation handling of the params.
Command used and terminal output
Relevant files
No response
System information
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