search

refgenie / refgenconf

A Python object for standardized reference genome assets.
http://refgenie.databio.org
BSD 2-Clause "Simplified" License
3 stars 6 forks source link

tags in `RefGenConf.populate`? #125

Closed stolarczyk closed 3 years ago

stolarczyk commented 3 years ago

It appears that RefGenConf.populate does not respect tags. Note the :test string appended to the output path below.

In [1]: from refgenconf import RefGenConf

In [2]: rgc = RefGenConf("g.yml")

In [3]: rgc.populate(glob="refgenie://rCRSd/fasta:test")
Out[3]: '/Users/mstolarczyk/Desktop/testing/refgenie/alias/rCRSd/fasta/default/rCRSd.fa:test'

also: https://github.com/refgenie/refgenconf/runs/2270085297#step:8:59

Is that intentional?

Changing the regex from "refgenie://([A-Za-z0-9_/\.]+)?" to "refgenie://([A-Za-z0-9_/\.\:]+)?" solves the issue.

nsheff commented 3 years ago

Not intentionally -- I just didn't test it with tagged assets. So, I think your change is probably correct

stolarczyk commented 3 years ago

ok, that's what I thought. Just wanted to make sure it's not sth related to nfcore usages etc.