Pipeline fails when using a relative path for base_index_path

[szymonwieloch]

Normally when you use the --base_index_path parameter, you want to use a relative path, something like:

nextflow nf-core/hlatyping --base_index_path hla_ref_dir

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

path(data_index) from params.base_index_path

I believe that path() accepts only absolute paths. The workaround is to use file:

file(data_index) from file(params.base_index_path)

[christopher-mohr]

Solved by #140.