Minimum inputs

The key words “MUST”, “MUST NOT”, “SHOULD”, etc. are to be interpreted as described in RFC 2119.

Pipelines MAY accept as many input files as needed, but it SHOULD be possible to run with as few as possible.

Pipelines SHOULD auto-generate missing reference files where possible. For example, given a reference genome Fasta file a pipeline would build the reference index files. The pipeline SHOULD also be able to optionally accept the reference index files if available.