Hi @Alysha
If you mapped against GRCh38 using a public Galaxy server, then yes, it was (probably) the UCSC version of the assembly/build named hg38. But you can check – how to is below.
For the assembly version, UCSC based their build of hg38 on the original release (not later patches/updates): http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/
Full details about UCSC’s source for the assembly are covered in the documents in their Downloads area plus there is a summary in the UCSC Genome Browser itself (check the home page for the human/hg38 genome at https://genome.ucsc.edu/cgi-bin/hgGateway). That is the same version as indexed for tools at usegalaxy.* public Galaxy servers: usegalaxy.org, usegalaxy.eu, and usegalaxy.org.au.
- http://hgdownload.soe.ucsc.edu/downloads.html#human >> Genome sequence files and select annotations (2bit, GTF, GC-content, etc)
For many tools, reference genome indexes for hg38 will be built-in at public Galaxy servers but reference annotation for hg38 will need to be supplied by you from the history as a dataset. The reference annotation datatype required by tools can differ. Most use a gtf datatype – but in the case of RSeQC, the tool requires a bed datatype with 12 columns.
UCSC is a good source for “bed12” annotation (will have the bed datatype assigned and should be the 12 column type, not 3, 4, or 6 columns). Importantly, the chromosome identifiers will match between the annotation (sourced from UCSC’s Table Browser) and the reference genome indexed in Galaxy (sourced from UCSC’s Downloads area).
If you didn’t map with BWA-MEM in Galaxy, or at a public Galaxy server other than the usegalaxy.* servers, some other build/version of the GRCh38 genome assembly may have been used.
These FAQs cover datatypes, expected formats, and related help, including how to make sure all of your inputs are a “match”. Using the same exact genome build/version for all analysis steps is important, otherwise tools can error or produce unexpected/scientifically incorrect results.
- Start here: https://galaxyproject.org/support/ >> https://galaxyproject.org/support/#getting-inputs-right
More help is also at this forum. Searching with keywords like “reference” or “annotation” or even “hg38” will find prior Q&A similar to yours 
Hope that helps!