geofetch
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pepkit
Builds a PEP from SRA or GEO accessions
Geofetch doesn't display its version in the help. all our other tools do this by using the VersionInHelpParser from ubiquerg. geofetch should also use this.
Docs were moved to pep.databio.org, This docs should be checked and updated
In general it is not recommended to use actual data in unit tests because it can make the tests less reliable and more difficult to maintain. (Especially, because data may...
config files produced by geofetch use this for derived attributes: ``` {SRABAM}{SRR} ``` But this only works if `{SRABAM}` has a trailing slash, which it may not. It should check...
At the moment, geofetch can download, filter, save metadata for the specific accessions in GEO. But metadata in GEO is stored in different, messy ways. Some of the information can...
Geofetch doesn't trim string of ref_genome, and it leads to issues later in pipelines