process_arguments: Processes the user input arguments
In ErikSchutte/leqtar: Linear eQTL analysis in R

Processes the user input arguments

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process_arguments(run_name, genotypeFile, genotypePositionFile, phenotypeFile,
  phenotypePositionFile, covariateFile, geneNames, useModel, output_dir,
  genoToFreq, forceRun)

`run_name`	Paramter that defines the name of the current run.
`genotypeFile`	A file/object containing genotypes.
`genotypePositionFile`	A file/object containing the positions for each SNP.
`phenotypeFile`	A file/object containing phenotypes.
`phenotypePositionFile`	A file/object containing the positions for each Gene.
`covariateFile`	A file/object contaning covariates for each sample in the genotype- and phenotype-File.
`geneNames`	A file containing the gene names that corrospond to Ensemble ID's or any other ID.
`useModel`	A string representing the model that should be used for QTL mapping.
`output_dir`	A path were the output from Leqtar is stored.
`genoToFreq`	A boolean flag, when set to 'TRUE' genotypes are converted to frequencies.
`forceRun`	A boolean flag, when set to 'TRUE' an already existing run can be overwritten.