Swap test file paths to use `testdata_base_path`

[SPPearce]

In the last few months we have swapped the file paths used in tests from:

file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)

to direct paths like:

file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)

This is in the guidelines now, but could do with a bulk update.

It would be great to have an automatic method to update all the filepaths at once, at least in the nf-test tests (but should be equivalent for pytest I think) This could do with a linting check too, to ensure that new modules (or pytest -> nf-test conversions) still keep this.