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Create R script that reads the Nextclade output from the Nanopore pipeline #4

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jonbra opened this issue Feb 9, 2024 · 3 comments

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jonbra commented Feb 9, 2024

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jonbra commented Feb 9, 2024 •

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

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jonbra commented Feb 9, 2024 •

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

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jonbra commented Feb 9, 2024

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.

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