Don't use absolute hard paths in output PEPs

pepkit / geofetch

Builds a PEP from SRA or GEO accessions

https://pep.databio.org/geofetch/

BSD 2-Clause "Simplified" License

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Don't use absolute hard paths in output PEPs #54

Closed nsheff closed 2 years ago

nsheff commented 2 years ago

Right now, when using --processed the PEP that is output uses a hard-coded absolute path to the sample table it creates. This makes the resulting PEP not portable.

Will the PEP allow a relative path? if so, can we instead use relative paths there?

e.g.