The Annotate Sequence with GFF File makes it very easy to annotate a sequence with annotations from a GFF file (Generic Feature Format). A GFF file does not contain any sequence information, it only contains a list of annotations. You can read more about the format at http://www.sanger.ac.uk/Software/formats/GFF.
You can also use GTF files (Gene Transfer Format). This format is used by among others the UCSC Genome Browser at http://genome.ucsc.edu . If you download an annotation track (e.g. SNPs, repeats) you can get this as a GTF file.
Note! GTF-files downloaded from the UCSC genome browser are not compatible with the RNA-Seq Analysis of CLC Genomics Workbench because the gene and transcript annotations cannot be matched. See examples, guides and read more about the plug-in in the GFF Plug-in User Manual