path of parcodes

clean.sh

+## remove all files generated by this workflow
+rm -Rf assembled log 
\ No newline at end of file

main.sh

@@ -21,3 +21,9 @@ snakemake -s scripts/step1.sf -j $CORES --latency-wait 120
 snakemake -s scripts/step2.sf -j $CORES --latency-wait 120
 snakemake -s scripts/step3.sf -j $CORES --latency-wait 120
 snakemake -s scripts/step4.sf -j $CORES --latency-wait 120
+
+
+snakemake -s Snakefile -j 8 --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk"
+
+
+rm -Rf assembled log 
\ No newline at end of file

rules/step1.smk

@@ -42,10 +42,11 @@ rule assign_sequences:
         config["container"]
     params:
         barcodeFile=lambda wcs: config["barcodeFiles"][wcs.run]
+        barcodeFolder=config['fastqFolderPath']
     log:
         'log/assign_sequences/{run}.log'
     shell:
-        '''ngsfilter -t {params.barcodeFile} -u {output.unid} {input[0]} --fasta-output > {output.assign} 2> {log}'''
+        '''ngsfilter -t {params.barcodeFolder}{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: