to run a snakemake pipeline:

enter project directory
cd to ARMOR directory
git pull origin master to be sure you have most update snakemake pipeline
conda activate ARMOR
snakemake -n --use-conda for a 'dry run'
snakemake -j 6 --use-conda for full run

try running all of this inside a tmux sesssion
if you get an error saying 'target cannot be locked', check to make sure that snakemake is not running elsewhere at the same time (probably in another tmux session)

to view all of the rules for a snakemake pipeline:

snakemake --rulegraph | dot -Tpdf > rulegraph.pdf