Add Results.R script for generating data for Labware 8 #51
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First commit of the Results.R script for LawWare 8. Please review. |
erinyoung
reviewed
Feb 25, 2025
| base_path<-config$paths$covidseq_base | ||
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| args = commandArgs(trailingOnly=T) | ||
| args[1]<-c("UT-VH00770-250214") |
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Does this need to be changed for each run?
erinyoung
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Feb 25, 2025
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| # saving results | ||
| write.table(results,paste("/Volumes/NGS/Analysis/covidseq/",args[1],"/",args[1], | ||
| "FinalResults.txt",sep=""), sep = ',', row.names = F, col.names = T, eol="\r\n", quote = F) | ||
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| write.table(results,paste("/Volumes/NGS/Analysis/covidseq/",args[1],"/",args[1], | ||
| "FinalResults.csv",sep=""), sep = ',', row.names = F, col.names = T, eol="\r\n", quote = F) | ||
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erinyoung
reviewed
Feb 25, 2025
| library("data.table");library("dplyr");library("utils"); | ||
| library("lubridate");find("read.table");library("readr"); | ||
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| config<-read_yaml("config.yml") |
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Are we going to be editing the config file a lot?
erinyoung
reviewed
Feb 25, 2025
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| library("data.table");library("dplyr");library("utils"); | ||
| library("lubridate");find("read.table");library("readr"); |
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Are these installed in prod already?
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Could you add a paragraph in the readme about how and when to use this script? |
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This PR introduces the Results.R script, which extracts and formats sequencing data for Labware 8. The output includes these fields: LIMS_TEST_ID, Run Name, Submission ID, Non-Ambiguous Bases, Nextclade Clade, and Lineage. This script ensures that the necessary data is structured appropriately for integration into Labware 8.