added analyse gatk steps analyse covariants/ variant calling/ snpeff variantannotator annotations

 Changes to be committed:
	modified:   GenerateScripts.sh
	modified:   parameters.csv
	modified:   protocols/FluxCapacitor.sh
	new file:   protocols/GatkAnalyseCovariants.sh
	new file:   protocols/GatkHaplotypeCaller.sh
	new file:   protocols/GatkSnpEffVariantAnnotation.sh
	modified:   workflow.csv
rename because the file had minor clash with protocols folder
 Changes to be committed:
	renamed:    projectsamplesheet.csv -> samplesheet.csv