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Rules to run fastp / Snakemake !
By Abhi 1133 days ago
rule fastp:
input:
fwd=INPUT + "/{sample}-read_1.fq",
rev=INPUT + "/{sample}-read_2.fq"
output:
fwd=RESULTS + "/fastq_trimmed/{sample}.1.trimmed.fastq",
rev=RESULTS + "/fastq_trimmed/{sample}.2.trimmed.fastq",
html=RESULTS + "/fastq_trimmed/{sample}.html",
json=RESULTS + "/fastq_trimmed/{sample}.json"
threads:
5
log:
RESULTS + "/logs/fastp/{sample}.preprocess.log"
shell:
"fastp --in1 {input.fwd} --in2 {input.rev} "
"--out1 {output.fwd} --out2 {output.rev} --thread {threads} --cut_tail --html {output.html} --json {output.json} 2> {log}"
