Usage

Just run the wrapper 🐍

The provided Snakefiles and rules have everything required to run the pipeline.

• LepMap3: you will need to create a pedigree file and have your filtered VCF ready.
• LepAnchor: you will need a linkage map and a genome assembly

To run the software, make sure you are in a conda environment with Snakemake installed (preferably the environment LepWrap creates via conda), and it will be as simple as entering this command in the working directory:

LepWrap <number_of_cores> <config.yml>

# example #
LepWrap 16                    # assumes config.yml
LepWrap 8 morgandistance.yml  # specific config file

where <number_of_cores> is the total number of threads you want Snakemake to scale for and <config.yml> (optional!) is the name of the config file, if it's different than config.yml. 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 LepMap3 and LepAnchor independently

Both LepMap3 and LepAnchor have their own separate snakemake pipelines*, meaning you can run them independently. If you only want to run one, you can toggle it on/off in the config file under the paremeters run_lepmap: and run_lepanchor:.

*although the LepAnchor requires the distances/intervals output at the end of LepMap3