In the server of reference genomes that we use in nf-core our genome names contain dashes (e.g. sus_scrofa-ucsc-susscr2).
The regular expression that is used to extract those names for populate of Refgenie registry paths does not allow dashes, making the command fail.
Would it be possible to allow dashes in the genome names?
No local digest for genome alias: None
Setting 'None' identity with server: http://igenomes.databio.org/v3/genomes/genome_digest/None
Genome 'None' not available on any of the following servers: http://igenomes.databio.org
'refgenie://homo_sapiens' refgenie registry path not populated.
Hi!
In the server of reference genomes that we use in nf-core our genome names contain dashes (e.g. sus_scrofa-ucsc-susscr2). The regular expression that is used to extract those names for populate of Refgenie registry paths does not allow dashes, making the command fail.
Would it be possible to allow dashes in the genome names?
Thank you!
test_igenomes.config.tpl
Command used:
refgenie populater --file test_igenomes.config.tpl
Error message:
Output:
Changing the regex to
refgenie://([A-Za-z0-9_\-/\.\:]+)?
outputs the expected file populated with remote links:This issue is realted to: https://github.com/nf-core/tools/issues/1084