Commit aa8d7e69 authored by peguerin's avatar peguerin
Browse files

path of parcodes

parent b550ff89

clean.sh

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## remove all files generated by this workflow

rm -Rf assembled log 
 No newline at end of file

main.sh

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@@ -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

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@@ -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: