folder path

rules/step1.smk

@@ -5,8 +5,8 @@ __license__ = "MIT"
 ### Paired end alignment then keep reads with quality > 40
 rule illuminapairedend:
     input:
-        R1=config['fastqFolderPath']+'{run}_R1.fastq.gz',
-        R2=config['fastqFolderPath']+'{run}_R2.fastq.gz'
+        R1='{run}_R1.fastq.gz',
+        R2='{run}_R2.fastq.gz'
     output:
         fq='assembled/{run}/{run}.fastq'
     singularity:
@@ -14,9 +14,10 @@ rule illuminapairedend:
     log:
         'log/illuminapairedend/{run}.log'
     params:
+        folderFastq=config['fastqFolderPath']
         s_min=config["illuminapairedend"]["s_min"]
     shell:
-        '''illuminapairedend -r {input.R2} {input.R1} --score-min={params.s_min} > {output.fq} 2> {log}'''
+        '''illuminapairedend -r {params.folderFastq}{input.R2} {params.folderFastq}{input.R1} --score-min={params.s_min} > {output.fq} 2> {log}'''
 
 ### Remove unaligned sequence records
 rule remove_unaligned:
@@ -43,8 +44,10 @@ rule assign_sequences:
         config["container"]
     log:
         'log/assign_sequences/{run}.log'
+    params:
+        folderBarcodes=config['fastqFolderPath']
     shell:
-        '''ngsfilter -t {input[1]} -u {output.unid} {input[0]} --fasta-output > {output.assign} 2> {log}'''
+        '''ngsfilter -t {params.folderBarcodes}{input[1]} -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: