Commit aa8d7e69 authored by peguerin's avatar peguerin

path of parcodes

parent b550ff89
## remove all files generated by this workflow
rm -Rf assembled log
\ No newline at end of file
......@@ -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
......@@ -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:
......
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