Make nb_inds param required for simulation + fix snk syntax

cnvpipelines.py

@@ -1287,7 +1287,7 @@ if __name__ == "__main__":
 
     # ---Simulation
     simul_parser = run_parsers.add_parser("simulation", help="Run a complete simulation workflow")
-    simul_parser.add_argument("-nb", "--nb-inds", help="Number of individuals to generate", type=int)
+    simul_parser.add_argument("-nb", "--nb-inds", help="Number of individuals to generate", type=int, required=True)
     simul_parser.add_argument("-r", "--reference", help="Reference genome", required=True)
     simul_parser.add_argument("-ns", "--nstretches", help="N-stretches positions bed file", required=False)
     simul_parser.add_argument("-s", "--sv-list", help="File containing the SVs", required=False)

snakecnv/popsim.snk

@@ -100,7 +100,7 @@ rule get_fasta_popsim:
 
 rule buildpop:
     input:
-        ".filter-chrs"
+        ".filter-chrs",
         **bp_inputs
     output:
         *bp_outputs,