From ce933c5532f6f92b95df44bad41857e53df1229c Mon Sep 17 00:00:00 2001
From: BIOPZ-Katsantoni Maria <maria.katsantoni@unibas.ch>
Date: Fri, 21 Feb 2020 12:56:56 +0100
Subject: [PATCH] Fixed required argument
---
scripts/labkey_to_snakemake.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/scripts/labkey_to_snakemake.py b/scripts/labkey_to_snakemake.py
index f538895..4456e00 100755
--- a/scripts/labkey_to_snakemake.py
+++ b/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",
--
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