Entrypoints

This pipeline has three entrypoints, 'parser', 'gvf', and 'fasta'. When using the 'parser' entrypoint, the raw files from variant callers are expected and corresponding moPepGen parsers are called before running callVariant. When using the 'gvf' entrypoint, the moPepGen GVF files are expected and moPepGen callVariant is called directly on them. When using the 'fasta' entrypoint, not only the moPepGen GVF files are expected from the input_csv, but also variant peptide FASTA file needs to be input to the pipeline. It then skips callVariant and only the downstream filterFasta, splitFasta, encodeFasta and summarizeFasta are called.

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