Added --version parameter

hisat2-pipeline

@@ -1,5 +1,6 @@
 #! python
 import os, glob, gzip, re, argparse
+version_string = "HISAT2-pipline v1.0.6 (2023/12) "
 
 class Sample:
 
@@ -558,17 +559,10 @@ def checkIfAllPrerequisitesInstalled():
 		print("Make sure it is installed, and that you're")
 		print("running this script in the same environment.")
 		print("Quitting...")
-		quit()
+		exit(130)
 	else:
 		print("... no problems found.")
 		print("")
-
-
-
-print("HISAT2-pipline - Version 1.0.6 (2023/12) ")
-print("")
-
-
 
 
 parser = argparse.ArgumentParser()
@@ -578,9 +572,17 @@ parser.add_argument("--outfolder", help="The folder where the results will be wr
 parser.add_argument("--skip_mapping", help="Skip mapping to genome", action="store_true")
 parser.add_argument("--threads", help=f"The number of threads used (default={os.cpu_count()})", default=f"{os.cpu_count()}")
 parser.add_argument("--yes", help="Answer all questions with 'yes'", action='store_true')
+parser.add_argument("--version", help="Prints the current version'", action='store_true')
 
 args = parser.parse_args()
 
+
+print(version_string)
+print("")
+
+if args.version:
+	exit(0) #exit immediately after printing the version
+
 folder = args.outfolder
 
 reads_folder = args.reads_folder
@@ -597,7 +599,7 @@ all_read_files = [f for f in glob.glob(f"{reads_folder}/*") if isFastqFile(f)]
 if len(all_read_files)==0:
 	print(f"Found no reads in reads folder ({reads_folder})")
 	print("Quitting...")
-	quit()
+	exit(130)
 
 PAIRED = arePairedReads(reads_folder)
 if PAIRED:
@@ -611,7 +613,7 @@ else:
 	if "N" in paired_correct_answer.upper():
 		print("Please rename the file so that they contain _R1 and _R2 respectively (or _Read1 and _Read2). Otherwise I won't able to distinguish them.")
 		print("Exiting")
-		quit()	
+		exit(0)	
 
 if PAIRED:
 	print("Running pipeline with PAIRED reads")
@@ -630,15 +632,15 @@ print()
 samples_correct = "yes" if args.yes else input("Is this correct? (yes/no) ")
 if "n" in samples_correct.lower():
 		print("Exiting")
-		quit()	
+		exit(130)	
 
 
 print()
 gff_file = getGFFFile(genome_folder)
 if gff_file is None:
 	print("Could not find the GFF file for the genome. Are you sure it's in the genome folder?")
 	print("Quitting..")
-	quit()
+	exit(130)
 
 
 genome = lookForGenome(genome_folder)
@@ -659,7 +661,7 @@ if genome is not None:
 
 else:
 	print("Could not find a genome file in the genomes folder. Exiting")
-	quit()
+	exit(130)
 
 
 print()