Commit 1a62992f authored by peguerin's avatar peguerin

format snakemake

parent 8593bfc4
......@@ -5,8 +5,8 @@ __license__ = "MIT"
### 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:
......@@ -14,10 +14,9 @@ rule illuminapairedend:
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:
......
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