add config

00-rules/filtered.smk

@@ -18,8 +18,8 @@ rule goodlength_samples:
     log:
         '../99-log/06-goodlength_samples/{sample}.log'
     params:
-         count=config["good_length_samples"]["count"],
-         seq_length=config["good_length_samples"]["seq_length"]
+        count=config["good_length_samples"]["count"],
+        seq_length=config["good_length_samples"]["seq_length"]
     shell:
         '''obigrep  -p 'count>{params.count}' -s '^[ACGT]+$' -p 'seq_length>{params.seq_length}' {input} > {output} 2> {log}'''
 

02-demultiplex/Snakefile

 __author__ = "Pierre-Edouard Guerin"
 __license__ = "MIT"
 
+configfile: "../config.yaml"
+
 
 SAMPLES, = glob_wildcards('01-raw/{sample}.fasta')