format snakemake

### Paired end alignment then keep reads with quality > 40

rule illuminapairedend:

    input:

        R1='{run}_R1.fastq.gz',

        R2='{run}_R2.fastq.gz'

        R1=config['fastqFolderPath']+'{run}_R1.fastq.gz',

        R2=config['fastqFolderPath']+'{run}_R2.fastq.gz'

    output:

        fq='assembled/{run}/{run}.fastq'

    singularity:

    log:

        'log/illuminapairedend/{run}.log'

    params:

        folderFastq=config['fastqFolderPath'],

        s_min=config["illuminapairedend"]["s_min"]

    shell:

        '''illuminapairedend -r {params.folderFastq}{input.R2} {params.folderFastq}{input.R1} --score-min={params.s_min} > {output.fq} 2> {log}'''

        '''illuminapairedend -r {input.R2} {input.R1} --score-min={params.s_min} > {output.fq} 2> {log}'''

### Remove unaligned sequence records

rule remove_unaligned: