Usage

If you are familiar with Snakemake

In the working directory:

snakemake --cores 16

where the number after --cores is the total number of threads you want Snakemake to scale for.

If you are unfamiliar with Snakemake

The provided Snakefile and rules in rules/*.smk 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:

snakemake --cores 16

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. LepMak3r provides rules to remove the files and folders associated with particular steps:

snakemake clean

Removes output generated from the entire pipeline, leaving only your vcf, pedigree, and config files intact.

snakemake clean_data

Removes data.call.gz and data_f.call.gz

snakemake clean_map

Removes map.master and maps.splitchrom/

snakemake clean_order

Removes the entire ordermarkers/ folder

snakemake clean_trim

Removes ordermarkers/best.trim/ and the associated logs

snakemake clean_reorder

Removes reordermarkers/

snakemake clean_distance

Removes intervals/, distances and distances/sexaverage