Commit 4cfc3cee authored by Midoux Cedric's avatar Midoux Cedric
Browse files

quality

parent 45493d70
{ {
"THREADS": 8, "THREADS": 8,
"MEM": 10 "MEM": 10,
"SAMPLES": ["4A", "5A", "6A", "7A", "8A", "9A", "10A", "11A", "12A"]
} }
configfile: "./config.json"
MEM=config["MEM"]
SAMPLES=config["SAMPLES"]
rule all:
input:
"report/multiqc_report.html"
include: "quality.smk"
rule fastqc:
input:
"DATA/{sample}.fastq.gz"
output:
zip = "work/fastqc/{sample}_fastqc.zip",
html = "work/fastqc/{sample}_fastqc.html"
params:
output = "work/fastqc/"
shell:
"fastqc "
"{input} "
"--noextract "
"--outdir {params.output} "
rule multiqc:
input:
expand("work/fastqc/{sample}_fastqc.zip", sample=SAMPLES)
output:
html = "report/multiqc_report.html",
params:
output = "report/"
shell:
"multiqc "
"--no-data-dir "
"--outdir {params.output} "
"{input} "
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