format rules

Snakefile

@@ -7,14 +7,14 @@ configfile: "config.yaml"
 rule all:
     input:
         expand("{folder}{run}_R1.fastq.gz", run=config["fastqFiles"],folder=config["fastqFolderPath"]),
-        expand('assembled/{run}/{run}.fastq', run=config["fastqFiles"]),
-        expand('assembled/{run}/{run}.ali.fastq', run=config["fastqFiles"]),
-        expand('assembled/{run}/{run}.ali.assigned.fastq', run=config["fastqFiles"]),
-        expand('assembled/{run}/{run}.unidentified.fastq', run=config["fastqFiles"]),
-        expand('log/remove_unaligned/{run}.log',run=config["fastqFiles"]),
-        expand('log/illuminapairedend/{run}.log',run=config["fastqFiles"]),
-        expand('log/assign_sequences/{run}.log',run=config["fastqFiles"]),
-        expand('log/split_sequences/{run}.log',run=config["fastqFiles"])
+        expand('01-assembly/{run}/{run}.fastq', run=config["fastqFiles"]),
+        expand('01-assembly/{run}/{run}.ali.fastq', run=config["fastqFiles"]),
+        expand('01-assembly/{run}/{run}.ali.assigned.fastq', run=config["fastqFiles"]),
+        expand('01-assembly/{run}/{run}.unidentified.fastq', run=config["fastqFiles"]),
+        expand('99-log/remove_unaligned/{run}.log',run=config["fastqFiles"]),
+        expand('99-log/illuminapairedend/{run}.log',run=config["fastqFiles"]),
+        expand('99-log/assign_sequences/{run}.log',run=config["fastqFiles"]),
+        expand('99-log/split_sequences/{run}.log',run=config["fastqFiles"])
 
-
-include: "rules/step1.smk"
\ No newline at end of file
+include: "00-rules/assembly.smk"
+include: "00-rules/demultiplex.smk"