Ref parsing WIP

src/preprocessing/2_parse_ref.r

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+library(Rsubread)
+library(sva)
+library(ballgown)
+
+# Function to get the directory of the current script
+get_script_dir <- function() {
+  cmdArgs <- commandArgs(trailingOnly = FALSE)
+  match <- grep("--file=", cmdArgs)
+  if (length(match) > 0) {
+    return(dirname(normalizePath(sub("--file=", "", cmdArgs[match]))))
+  } else {
+    return(dirname(normalizePath(sys.frames()[[1]]$ofile)))
+  }
+}
+
+# Define a constant REF_GENOME relative to the script's directory
+script_dir <- get_script_dir()
+REF_GENOME <- file.path(script_dir, "../../data/reference/Homo_sapiens.GRCh38.103.gtf")
+
+# Print the constant REF_GENOME
+cat("Reference Genome Path:", REF_GENOME, "\n")