digraph {
    compound = true
    node [shape = "box", style = "filled, rounded"]

    subgraph cluster_script {
        label = "scripts"

        node [color = lightskyblue]

        script_version_b[label = "nature-v2"]
    }

    subgraph cluster_data {
        label = "data repository (not git!)"

        node [color = limegreen]

        data_version_a[label = "doi:blah/blah"]
    }

    subgraph cluster_paper {
        label = "paper"

        node [color = limegreen]

        paper_version_c[label = "nature-final"]
    }

    paper_version_c -> data_version_a [label = "\n\n", lhead = cluster_data]

    data_version_a -> script_version_b [label = "\n\n", lhead = cluster_script]
}