To cite CAGEWorkflow in publications use:

  Thodberg et al, A step-by-step guide to analyzing CAGE data using
  R/Bioconductor, F1000Research 2019, 8:886

A BibTeX entry for LaTeX users is

  @Article{,
    title = {A step-by-step guide to analyzing CAGE data using R/Bioconductor.},
    author = {Malte Thodberg and Albin Sandelin},
    year = {2019},
    journal = {F1000Research},
    doi = {10.12688/f1000research.18456.1},
    volume = {8},
    issue = {644},
    pages = {886},
  }