nested

02-demultiplex/Snakefile

@@ -3,7 +3,9 @@ __license__ = "MIT"
 
 configfile: "../config.yaml"
 
-SAMPLES, = glob_wildcards('01-raw/{sample}.fasta')
+SAMPLES, = glob_wildcards('01-raw/{run}/{sample}.fasta')
+
+print(SAMPLES)
 
 rule all:
     input:
@@ -19,14 +21,3 @@ rule all:
 
 include: "../00-rules/filtered.smk"
 
-
-### Concatenate sequences from each sample of the same run
-rule cat_samples:
-    input:
-        glob_wildcards('03-cleaned/{run}*.c.r.l.u.fasta'
-    params:
-        '03-cleaned/{run}*.c.r.l.u.fasta'
-    output:
-        '../03-filtered/{run}.fasta'
-    shell:
-        '''cat {params} > {output}'''
\ No newline at end of file