Configuration

In Snakemake, the most rational way to augment rules/runs is through a config file. This prevents hard-coding rules, and making direct changes to them that may break something. That would be a problem because with Snakemake, breaking something breaks everything.

The config.yaml

LepMak3r provides an aggressively annotated config.yaml for you to replace parameters in as necessary. There are currently 13 parameters to specify, with an explanation for each. Only change the parameter value, do not change the parameter name. The Snakefile handles reading all these parameters in accordingly. Let's look at the first few lines of the file as an example:

# Configuration file for LepMak3r

#---------------#
#  ParentCall2  #
#---------------#
# the filtered VCF file with your genotype likelihoods:
vcf: "YFT70_maxmiss80.recode.vcf"

# Instructions to create pedigree file: https://sourceforge.net/p/lep-map3/wiki/LM3 Home/#parentcall2
# the pedigree file associated with your data
pedigree: "pedigree.txt"

There's a lot of text, and most of it is annotations (# denote comments in yaml). Since everything happens out of the working directory, you need only to specify a relative path to the files. Personally, I keep these two files in the working directory, so as to minimize the possibility of typos in path names, but to each their own.

The remainder of the file reads similarly, so it shouldn't be too difficult to figure out what is what.