From 392928345e48cb97fc463328eabd8bcff6e5827d Mon Sep 17 00:00:00 2001
From: Joe Brown <brwnjm@gmail.com>
Date: Wed, 31 Oct 2018 16:42:03 -0700
Subject: [PATCH] fixes #17

---
 hundo/Snakefile   | 2 +-
 hundo/__init__.py | 2 +-
 hundo/hundo.py    | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/hundo/Snakefile b/hundo/Snakefile
index d6a4baf..aac3839 100644
--- a/hundo/Snakefile
+++ b/hundo/Snakefile
@@ -247,7 +247,7 @@ def md5(fname):
 
 PROTOCOL_VERSION = subprocess.check_output("hundo --version", shell=True).decode("utf-8").strip()
 if config.get("workflow") == "download":
-    SAMPLES, OMITTED = {"placeholder": {"r1": "placeholder", "r2": "placeholder"}}
+    SAMPLES, OMITTED = ({"placeholder": {"r1": "placeholder", "r2": "placeholder"}}, dict())
 else:
     SAMPLES, OMITTED = get_sample_files(
         config.get("fastq_dir"), config.get("prefilter_file_size", 100000)
diff --git a/hundo/__init__.py b/hundo/__init__.py
index a955fda..10aa336 100644
--- a/hundo/__init__.py
+++ b/hundo/__init__.py
@@ -1 +1 @@
-__version__ = "1.2.1"
+__version__ = "1.2.3"
diff --git a/hundo/hundo.py b/hundo/hundo.py
index a738db1..8a4f5c2 100644
--- a/hundo/hundo.py
+++ b/hundo/hundo.py
@@ -192,7 +192,7 @@ def get_snakefile():
     help="use at most this many cores in parallel",
 )
 @click.option(
-    "--rd",
+    "-rd",
     "--reference-database",
     default="silva",
     type=click.Choice(["silva", "greengenes", "unite"]),