format snakemake

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

@@ -35,18 +35,17 @@ rule remove_unaligned:
 rule assign_sequences:
     input:
         'assembled/{run}/{run}.ali.fastq',
-        lambda wildcards: config["barcodeFiles"][wildcards.run]
     output:
         assign='assembled/{run}/{run}.ali.assigned.fastq',
         unid='assembled/{run}/{run}.unidentified.fastq'
     singularity:
         config["container"]
+    params:
+        barcodeFile=lambda wcs: config["barcodeFiles"][wcs.run]
     log:
         'log/assign_sequences/{run}.log'
-    params:
-        folderBarcodes=config['fastqFolderPath']
     shell:
-        '''ngsfilter -t {params.folderBarcodes}{input[1]} -u {output.unid} {input[0]} --fasta-output > {output.assign} 2> {log}'''
+        '''ngsfilter -t {params.barcodeFile} -u {output.unid} {input[0]} --fasta-output > {output.assign} 2> {log}'''
 
 ### Split the input sequence file in a set of subfiles according to the values of attribute `sample`
 rule split_sequences: