path from config

Snakefile

@@ -6,7 +6,7 @@ configfile: "config.yaml"
 
 rule all:
     input:
-        expand("{folder}/{run}_R1.fastq.gz", run=config["fastqFiles"],folder=config["fastqFolderPath"]),        
+        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"]),

rules/step1.smk

@@ -5,8 +5,8 @@ __license__ = "MIT"
 ### Paired end alignment then keep reads with quality > 40
 rule illuminapairedend:
     input:
-        R1='raw/{run}_R1.fastq.gz',
-        R2='raw/{run}_R2.fastq.gz'
+        R1=config['fastqFolderPath']+'{run}_R1.fastq.gz',
+        R2=config['fastqFolderPath']+'{run}_R2.fastq.gz'
     output:
         fq='assembled/{run}/{run}.fastq'
     singularity: