Epidisco is a highly-configurable genomic pipeline. It supports alignment, the GATK, variant calling, epitope discovery, and vaccine generation.
Note on Multiple Samples
You can pass multiple samples into Epidisco, but they will be merged into one sample (tumor, normal, or tumor RNA) after the alignment & mark duplicates step. This option to process multiple samples should only be used to e.g. pass data from biological replicates (or samples you wish to treat as such) into the pipeline, which fundamentally operates on a tumor, normal, and tumor RNA sample set.