Commit 036f2fcf authored by peguerin's avatar peguerin

folder path

parent 7f99a5b4
......@@ -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:
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment