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Cedric Midoux
deepomics16S
Commits
4cfc3cee
Commit
4cfc3cee
authored
Apr 04, 2019
by
Cedric Midoux
Browse files
quality
parent
45493d70
Changes
3
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config.json
View file @
4cfc3cee
{
"THREADS"
:
8
,
"MEM"
:
10
"MEM"
:
10
,
"SAMPLES"
:
[
"4A"
,
"5A"
,
"6A"
,
"7A"
,
"8A"
,
"9A"
,
"10A"
,
"11A"
,
"12A"
]
}
global.smk
0 → 100644
View file @
4cfc3cee
configfile: "./config.json"
MEM=config["MEM"]
SAMPLES=config["SAMPLES"]
rule all:
input:
"report/multiqc_report.html"
include: "quality.smk"
quality.smk
0 → 100644
View file @
4cfc3cee
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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