Epidisco is a highly-configurable genomic pipeline. It supports alignment, the GATK, variant calling, epitope discovery, and vaccine generation.
It uses Biokepi to construct Ketrew workflows which can be scheduled on many kinds of clusters.
Documentation on Biokepi workflows is centralized in the project
hammerlab/wobidisco; a good starting
point is the “Running Local”
tutorial.
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.