Handle polyA processing in input preparation script

• fixes some functions in labkey_to_snakemake.py
• add optional argument for trimming polyA tails; they are trimmed as follows:
  • if mate is sense, oligo-A is added to sample table for cutadapt rule to trim
  • if mate is antisense, oligo-T is added to sample table for cutadapt rule to trim
  • if option is set to --trim_polya, oligo-X stretch is added to sample table and cutadapt will not trim

Closes #37 (closed)

scripts/labkey_to_snakemake.py

@@ -34,7 +34,7 @@ def main():
     parser = ArgumentParser(description=__doc__,
                             formatter_class=RawTextHelpFormatter)
 
-    parser.add_argument("--genomes_path",
+    parser.add_argument("genomes_path",
                         help="Path containing the FASTA and GTF " +
                         " files for all organisms",
                         metavar="GENOMES PATH")
@@ -83,6 +83,7 @@ def main():
     parser.add_argument("--trim_polya",
                         type=int,
                         choices=[True, False],
+                        default=True,
                         help="Trim poly-As option")
 
     parser.add_argument("--multimappers",