diff --git a/Snakefile b/Snakefile index 729540ab8cec8a946e2542ba8d346fc1bd180888..1b28552a15456104888ed465d311a7dd2fd87acf 100755 --- a/Snakefile +++ b/Snakefile @@ -54,15 +54,10 @@ REQUIREMENTS IN DESIGN: # 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)] -print(filenames) + if not filenames : raise ValueError("Please provides input fastq files") -samples = [sub(config["input_mate"]+config["input_extension"], '', file) for file in filenames] -marks = [ x.strip() for x in (config["design"]["marks"]).split(",")] -conds = [ x.strip() for x in (config["design"]["condition"]).split(",")] -rep_flag = config["design"]["replicates"] -print(samples, marks, conds) #------------------------------------------------------- # paired-end data gestion @@ -81,7 +76,12 @@ else: else: raise ValueError("Please provides single or paired files only") - +#get sample names +filename_R1 = [ file for file in filenames if match(r'.*'+rt1+config["input_extension"]+'', file)] +samples = [sub(rt1+config["input_extension"], '', file) for file in filename_R1] +marks = [ x.strip() for x in (config["design"]["marks"]).split(",")] +conds = [ x.strip() for x in (config["design"]["condition"]).split(",")] +rep_flag = config["design"]["replicates"] # ----------------------------------------------- # get list of INPUT files