The SMASH graphs produced by the smash program are not ideal for publication, especially considering we would like to highlight areas of interest which is not a supported feature of the builtin figure generation.
This Nextflow script and associated code utilize the raw data used by smash to produce more refined and modifiable graphs via conda, R, and ggplot2.
This workflow has been designed such that only nextflow and conda should be necessary -- all other dependencies are setup as needed.
$ nextflow -version
N E X T F L O W
version 22.04.5 build 5708
created 15-07-2022 16:09 UTC (12:09 EDT)
cite doi:10.1038/nbt.3820
http://nextflow.io
$ conda --version
conda 4.14.0