Drop JH-2-009 Sample due to contamination

Author: jjacobson95

build/mpnst/00_sample_gen.R

@@ -10,14 +10,12 @@ if(length(args) > 1 ){
     stop("Up to one argument is allowed. This is the filepath to the previously run samples file.")
 }
 
-
 if (length(args) == 0 || is.na(args[1]) || args[1] == "" || !file.exists(args[1])) {
     orig_samples <- ""
 } else {
     orig_samples <- fread(args[1])
 }
 
-
 # Check if Synapse token is available from the environment
 synapse_token <- Sys.getenv("SYNAPSE_AUTH_TOKEN")
 if (synapse_token == "") {
@@ -28,6 +26,10 @@ synapser::synLogin(authToken=synapse_token)
 manifest<-synapser::synTableQuery("select * from syn53503360")$asDataFrame()|>
                                                              as.data.frame()
 
+#Drop contaminated sample JH-2-009
+manifest <- manifest %>% 
+  filter(Sample != "JH-2-009")
+
 
 ###sample file has a strict schema
 ## - improve_sample_id
@@ -61,31 +63,13 @@ main<-rbind(sampTable,pdxmt)|>
     dplyr::select(-MicroTissueDrugFolder)|>
     rbind(tumorTable)
 
-#main <- fread("mpnst/NF_MPNST_samples.csv")
-#previous_aml <- fread(args[1])#"beatAML/beataml_samples.csv")
-
 # If there is no previous samples file - start at 1, else, continue where the previous one left off.
 if (identical(orig_samples, "")) {
     max_id <- 1  
 } else {
     max_id <- max(orig_samples$improve_sample_id, na.rm = TRUE)
 }
 
-
 main$improve_sample_id <- seq(from = max_id + 1, length.out = nrow(main))
 
-#synapse_main <- fread("mpnst/synapse_NF-MPNST_samples.csv")
-# Step 1: Create a dictionary from 'main'
-#id_dict <- setNames(main$improve_sample_id, main$other_id)
-
-# Step 2: Update 'ID' in 'synapse_main'
-#synapse_main$ID <- id_dict[synapse_main$Sample]
-
-# Handling NA values if any mismatch occurs (Optional based on your data integrity)
-# If there are NAs generated, you might need to check for unmatched keys
-# synapse_main$ID[is.na(synapse_main$ID)] <- -1  # Assign a placeholder like -1 for unmatched rows
-
-# Step 3: Save the updated 'synapse_main'
-#fwrite(synapse_main, "mpnst/synapse_NF-MPNST_samples.csv")
-#fwrite(main, "mpnst/NF_MPNST_samples.csv") # updated sample file
 fwrite(main,'/tmp/mpnst_samples.csv')