Consider adapting long formats for output files

[alexg9010]

Some of the output tables of the pipeline contain fixed and flexible column names.
Examples files from the test data would be (folder [tests/output]):

• mutations/data_mutation_plot.csv
• mutation_counts.csv
• mutations/Test0_mutations.csv
• variants/Test0_variants_with_meta.csv
• variants/data_variant_plot.csv

One location in the code where this format is created would be here:

pigx_sars-cov-2/scripts/deconvolution.R

Lines 490 to 497 in 485f7df

	# ensure metadata cols are first
	dplyr::select(all_of(c(
	"samplename",
	"dates",
	"location_name",
	"coordinates_lat",
	"coordinates_long"
	)), everything())

I would suggest converting these kinds of tables to long format, such that the table headers are static.
Should a wider format be required for plotting, reporting, etc. I would suggest doing the temporary transformation directly there.