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Commit 0a3aac85 authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
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Update Snakefile

parent 6a48dd58
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......@@ -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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