As of now, the default reference genome for the bulk RNAseq pipeline is Human (GRCh38.p14). However if the user wanted to change this, they are expected to supply the locations to all the relevant genome files inside config/references.config. This should be better simplified, where a user can specify "high-level" information about their reference (e.g. "Human", "Mouse"), the pipeline would then interpolate the information into the relevant filepaths for the reference genome.
As of now, the default reference genome for the bulk RNAseq pipeline is Human (GRCh38.p14). However if the user wanted to change this, they are expected to supply the locations to all the relevant genome files inside
config/references.config. This should be better simplified, where a user can specify "high-level" information about their reference (e.g. "Human", "Mouse"), the pipeline would then interpolate the information into the relevant filepaths for the reference genome.