Add optional parameters for all software to workflow

i.e.

		echo "Running plink command ..";
		plink ${true='--file ${file}' false='' withFile} \
			${true='--make-bed' false='' makeBed} \
			${true='--chr-set ${chrSet}' false='' withChrSet} \
			${true='' false='no-xy' withXY} \
			${true='' false='no-mt' withMt} \
			${true='' false='no-y' withY} \
			${true='--bfile ${filePrefix}' false='' withBfile} \
			${true='--indep-pairwise ${ldwinSize} ${ldwinStep} ${ldCuttoff}' false='' withIndepPairwise} \
			${true='--extract ${extractFile}' false='' extract} \
			${true='--out ${outFile}' false='' withOutFile} \
			${true='--recode ${rcFomat}' false='' withRecode};
		echo ". Done\n";
	}

Time pending: Needs to create boolean values for all parameters in json file