Build jflow commands: use absolute paths

build_jflow_command_line.py

 #!/usr/bin/env python
 
-import argparse
+import argparse, os
 
 parser = argparse.ArgumentParser(description='Generate simulated populations with SV')
 parser.add_argument("--nb-inds", help="Number of individuals to generate", required=True)
@@ -13,12 +13,14 @@ parser.add_argument("--bams-dir", help="Directory containing bams for each indiv
 args = parser.parse_args()
 
 nb_inds = args.nb_inds
-reference = args.reference
+reference = os.path.abspath(args.reference)
 bams_dir = args.bams_dir
 
 if bams_dir and bams_dir[-1] == "/":
     bams_dir = bams_dir[:-1]
 
+bams_dir = os.path.abspath(bams_dir)
+
 if not args.prepare and not args.bams_dir:
     print("You must specify the directory containing the bam files (--bams-dir)")
     exit(1)