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.

The Before and After

So you understand what to expect during a run, here is what the working directory should look like before you start. Notice that you will need to provide the filtered vcf and pedigree files. You can name them whatever you want, as long as you use their correct names in the config.yaml.

Folder_name
├── config.yaml
├── filtered_data.vcf
├── pedigree_file.txt
├── Snakefile
├── LM3      # directory of the Lep-Map3 modules
├── rules    # directory of the rule files
├── scripts  # directory of the Bash, R, and extra conversion scripts

and when LepMak3r finishes, your directory structure will look like this:

(files omitted for clarity, only showing folders):

Folder_name
├── distances
├── distances_sexaverage
│   └── logs
├── intervals
│   └── logs
├── LM3
├── maps.splitchrom
├── ordermarkers
│   ├── best.trim
│   ├── iterations
│   └── logs
│       ├── recombination
│       ├── runs
│       └── trimming
├── reordermarkers
│   ├── iterations
│   └── logs
│       ├── recombination
│       └── runs
├── rules
├── scripts

The folder structure for ordermarkers and reordermarkers are similar, except that reordermarkers does not have a trimming step, and therefore doesn't include any trimming folders. For ordermarkers, the folder will look like this:

ordermarkers
├── best.likelihoods
├── best.trim
│   ├── ordered.1.trimmed
│   ├── ordered.2.trimmed
│   ├── ordered.3...
├── iterations
│   ├── ordered.1.1
│   ├── ordered.1.2
│   ├── ordered.1...
├── logs
│   ├── recombination
│   │   ├── ordered.1.1.recombination
│   │   ├── ordered.1.2.recombination
│   │   ├── ordered.1.3...
│   ├── runs
│   │   ├── ordered.1.1.log
│   │   ├── ordered.1.2.log
│   │   ├── ordered.1.3...
│   ├── trimming
│   │   ├── ordered.1.1.removed
│   │   ├── ordered.1.1.trim.pdf
│   │   ├── ordered.1.2.removed
│   │   ├── ordered.1.2.trim.pdf
│   │   ├── ordered.1.3...
├── likelihoods.summary
├── recombination.summary
├── trim.summary

And reordermarkers will look the same, minus the trimming parts.