Commit 80ceae2f authored by Midoux Cedric's avatar Midoux Cedric
Browse files

quality.smk

parent 6cbd129f
......@@ -6,6 +6,6 @@ configfile: "./config.json"
rule all:
input:
"",
"report/multiqc_report.html",
include: "../workflow_metagenomics/*.smk"
include: "../workflow_metagenomics/quality.smk"
rule fastqc:
input:
"DATA/raw/{reads}.fastq.gz"
output:
zip = "work/fastqc/{reads}_fastqc.zip",
html = "work/fastqc/{reads}_fastqc.html"
params:
output = "work/fastqc/"
shell:
"fastqc "
"{input} "
"--noextract "
"--outdir {params.output} "
rule multiqc:
input:
expand("work/fastqc/{sample}_{R}_fastqc.zip", sample=config["SAMPLES"], R=["R1", "R2"]),
#expand("work/fastp/{sample}_fastp.json", sample=config["SAMPLES"])
output:
html = "report/multiqc_report.html",
params:
output = "report/"
shell:
"multiqc "
"--force "
"--no-data-dir "
"--outdir {params.output} "
"{input} "
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