From 0a3aac858c5882a95a3026472b8204485296e055 Mon Sep 17 00:00:00 2001
From: Rachel LEGENDRE <rachel.legendre@pasteur.fr>
Date: Wed, 9 Feb 2022 15:04:36 +0100
Subject: [PATCH] Update Snakefile
---
Snakefile | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index d169fdd..8843c47 100755
--- a/Snakefile
+++ b/Snakefile
@@ -27,6 +27,7 @@ import pandas as pd
from fnmatch import fnmatch
from re import sub, match
from itertools import repeat, chain
+import glob
import os
@@ -40,7 +41,7 @@ RULES = os.path.join("workflow", "rules")
#-------------------------------------------------------
# list of all files in the directory 'input_dir'
-filenames = [f for f in os.listdir(config["input_dir"]) if match(r'.*'+config["input_mate"]+config["input_extension"]+'', f)]
+filenames = [f for f in glob.glob(config["input_dir"]) if match(r'.*'+config["input_mate"]+config["input_extension"]+'', f)]
if not filenames :
raise ValueError("Please provides input fastq files")
--
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