README.md

Routes of analysis

All three routes of analysis are implemented as Nextflow DSL2 workflows and use the same style samplesheet. The name of the workflow (one of "two_references", "one_reference", and "arbitrary_grid") is specified when the pipeline is invoked:

  nextflow run main.nf [...] --workflow="two_references"

JAX users can edit the file submit.sb to specify the workflow.