Refactored code

Author: nkongenelly

bin/get_metadata.py

@@ -149,12 +149,6 @@ def get_demultiplexing_info(self):
     parser.add_argument(
         "--runfolder", type=str, required=True, help="Path to runfolder"
     )
-    parser.add_argument(
-        "--demultiplexer-outdir",
-        type=str,
-        default="Data/Intensities/BaseCalls",
-        help="Path to demultiplexer output folder relative to the runfolder",
-    )
 
     args = parser.parse_args()
     runfolder = args.runfolder

main.nf

@@ -49,7 +49,7 @@ def helpMessage() {
 
     Optional parameters:
         --result_dir                        Path to write results (default: results)
-        --demultiplexer_outdir              Folder name to check for fastq.gz files and demultiplexing stats (default: Data/Intensities/BaseCalls)
+        --demultiplexer_outdir              Folder name to check for fastq.gz files and demultiplexing stats (default: Unaligned)
         --checkqc_config                    Configuration file for CheckQC
         --assets_dir                        Location of project assests (default: "\$baseDir/assets").
         --config_dir                        Location of tool configuration files (default: "\$baseDir/config/tool_config").