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oschwengers / asap

A scalable bacterial genome assembly, annotation and analysis pipeline
https://doi.org/10.1371/journal.pcbi.1007134
GNU General Public License v3.0
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Error: wrong characters in strain (1)! #4

Closed marade closed 4 years ago

marade commented 4 years ago

I used the -c option to check my configuration input and received this cryptic error. How does one debug this?

oschwengers commented 4 years ago

Thanks @marade for pointing at this and filing this issue. It means that the strain designation within the config file contains invalid characters. Only alpha-numerics, '-' and '.' are allowed with min and max length of 2 and 50, respectively.

The -c/--check option is a feature from the early development stage. I guess no one has used it so far... But indeed, this needs a solid review and leaves room for much improvement!

As I am writing, I'm improving the checks and rewriting the error messages. I'll test and upload a patch version as soon as possible. I'll let you know.

oschwengers commented 4 years ago

@marade , I just released a patch version v1.2.2 enhancing the check logic via -c/--check and improving the error messages.

This comes with an updated asap.tar.gz.

Sorry for the inconvenience, this was heavily overdue. I hope this helps. Please let me know, if there is more to improve - just reopen this issue or file another one.

marade commented 4 years ago

Thanks for the rapid response @oschwengers. I appreciate your help.