From 4a8e40f7331f61ba8b7038e8ad48f86018ac7dc6 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 23 Sep 2021 12:47:27 +0300
Subject: pass json file path as an arg

---
 scripts/wgcna_analysis.R | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/scripts/wgcna_analysis.R b/scripts/wgcna_analysis.R
index 73d0e3f..53b59d5 100644
--- a/scripts/wgcna_analysis.R
+++ b/scripts/wgcna_analysis.R
@@ -7,11 +7,20 @@ library(rjson)
 options(stringsAsFactors = FALSE);
 
 imgDir = Sys.getenv("GENERATED_IMAGE_DIR")
-
 # load expression data **assumes from json files row(traits)(columns info+samples)
 # pass the file_path as arg
+# pass the file path to read json data
+
+args = commandArgs(trailingOnly=TRUE)
+
+if (length(args)==0) {
+  stop("Argument for the file location is requires", call.=FALSE)
+} else {
+  # default output file
+  json_file_path  = args[1]
+}
 
-results <- fromJSON(file = "file_path.json")
+results <- fromJSON(file = json_file_path)
 
 
 # parse the json data input
-- 
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