Commit c79aa53b authored by Slaheddine Kastalli's avatar Slaheddine Kastalli
Browse files

Delete preprocess.smk

parent 95eb0173
rule cutadapt:
input:
"DATA/{sample}.fastq.gz"
output:
"work/cutadapt/{sample}.fastq.gz"
params:
five = lambda wildcards: config["FIVE_PRIMER"][wildcards.sample],
three = lambda wildcards: config["THREE_PRIMER"][wildcards.sample]
shell:
"conda activate cutadapt-2.5 "
"&& "
"cutadapt "
"-g {params.five} "
"-a {params.three} "
"--error-rate 0.1 "
"--discard-untrimmed "
"--match-read-wildcards "
"-o {output} "
"{input} "
"&& "
"conda deactivate"
rule filter:
input:
"work/cutadapt/{sample}.fastq.gz"
output:
"work/filter/{sample}.fastq.gz"
script:
"filterAndTrim.R"
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