Problem
Currently, it is not possible to specify genome assemblies and corresponding versions on a per-sample basis, making it cumbersome to run samples originating from the same or from different sources against different genome assemblies or versions (the workaround is to specify the genome and gene annotation files directly).
Possible solution
Allow for additional optional fields genome_assembly and resource_version in the sample table. If provided, HTSinfer-based source inference is disabled and genomepy is triggered to fetch the specified version of the specified assembly (or the default assembly for the sample source/organism, if provided), if not already available.
Problem
Currently, it is not possible to specify genome assemblies and corresponding versions on a per-sample basis, making it cumbersome to run samples originating from the same or from different sources against different genome assemblies or versions (the workaround is to specify the genome and gene annotation files directly).
Possible solution
Allow for additional optional fields
genome_assemblyandresource_versionin the sample table. If provided, HTSinfer-based source inference is disabled andgenomepyis triggered to fetch the specified version of the specified assembly (or the default assembly for the sample source/organism, if provided), if not already available.