Create a GitHub action to run validation

[andersgs]

Create a Using GitHub Action called validation.yml that will run the tool against all the validation genomes, and assert we get the right results.

I would add the assemblies into the repo (but we don't package them) to validations/data/<assembler_version>/<sample_id>/contigs.fa folder in the root folder.

Then add a csv with the expected results in validations/data/pcr-results.csv.

It will then need a small NextFlow pipeline that runs the latest lissero on the controls, and on each of the genomes.

It then compares the output of lissero with the expected output to assert they are the same.

I believe @kristyhoran has a template of what the validation report might look like, so the NextFlow pipeline would ideally output that in PDF. The plain text version of the filled in template (before conversion to PDF) would be committed to validations/reports/ along with a CSV of the raw data (i.e., the one row per sample with the sample ID, the expected result, the observed result, and whether they match or not.

The NextFlow pipeline should be in validations/validation.nf and the config file should be validations/config.nextflow.

I appreciate there is a lot to this issue. I would start with just getting the NextFlow pipeline working on a local clone of the repo, and then work towards getting it working with the GitHub Actions.