Usage

Just run the wrapper 🐍

The provided Snakefiles and rules in rules/ have everything required to run the pipeline. On your part, you will need to create a pedigree file and have your filtered VCF ready. To run the software, make sure you are in a conda environment with Snakemake installed, and it will be as simple as entering this command in the working directory:

./LepWrap <number_of_cores>

# example #
./LepWrap 16

where <number_of_cores> is the total number of threads you want Snakemake to scale for. Of course in this case 16 is just an example and you will need to provide the number of cores you would like it to use. Snakemake will then generate its job graph and perform the tasks as necessary to produce the distance files, all scaled to the number of cores you've allowed it to use. In the event a job gets interrupted, running Snakemake again will pick up at the rule it left off, so there shouldn't be a need to restart things from scratch.

Running LepAnchor too

The LepAnchor modules have their own snakefile to be able to easily toggle on/off whether you want to run it too. This can be set in the run_lepanchor: parameter in config.yaml:

####################
#### Lep-Anchor ####
####################
# change this to true if you also want to run Lep-Anchor
run_lepanchor: false