Create R script that reads the Nextclade output from the Nanopore pipeline

[jonbra]

See here: https://github.com/folkehelseinstituttet/FHI_SC2_Pipeline_Nanopore/blob/master/Binaries/SARS-CoV-2_Nanopore_Docker_V13.sh

[jonbra]

Use the file ${runname}_NextcladeAndPangolin.csv which is written on line 361.

[jonbra]

First draft created here: https://github.com/folkehelseinstituttet/SC2_drug_resistance/blob/master/drug_resistance.R Next steps:

• [ ] Read in the nextclade results file, including any variables for the file names
• [ ] Use the same variables to write the output.
• [ ] Merge the new columns in the final summary file that will be imported to BN
• [ ] Test the code on some real data.
• [ ] Test the BN import.