Usage

If you are familiar with Snakemake

The provided Snakefile 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:

./LepMak3r <number_of_cores>

# example #
./LepMak3r 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.

Cleaning steps

Sometimes you may want to redo something with different parameters, or clear out some files and folders because of a run ending prematurely so you can rerun the pipeline from a particular step. To accomplish that, do:

snakemake some_target delete-all-output --cores 1

although to be safe, you should do a dry run of that first:

snakemake some_target delete-all-output --cores 1 --dry-run