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Unfortunately this does not work. The error message in the log is strange and says something about a XML validation. Anyway, the same absolute path works fine. I believe that this line is responsible for the problem:
Normally when you use the
--base_index_path
parameter, you want to use a relative path, something like:Unfortunately this does not work. The error message in the log is strange and says something about a XML validation. Anyway, the same absolute path works fine. I believe that this line is responsible for the problem:
https://github.com/nf-core/hlatyping/blob/master/main.nf#L248
I believe that path() accepts only absolute paths. The workaround is to use file:
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