Commit 036f2fcf authored by peguerin's avatar peguerin
Browse files

folder path

parent 7f99a5b4

rules/step1.smk

+7 −4
Original line number Diff line number Diff line
@@ -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: