Failed to fetch fork details. Try again later.
-
Arnaud WATLET authored6d5bcb4d
Forked from
reversaal / OhmPi
Source project has a limited visibility.
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=SAMPLES, R=["R1", "R2"]),
expand("work/fastp/{sample}_fastp.json", sample=SAMPLES)
output:
html = "report/multiqc_report.html",
params:
output = "report/"
shell:
"multiqc "
"--force "
"--no-data-dir "
"--outdir {params.output} "
"{input} "