Commit f083191d authored by Slaheddine Kastalli's avatar Slaheddine Kastalli
Browse files

Delete quality.smk

parent c79aa53b
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:
"conda activate fastqc-0.11.8 "
"&& "
"fastqc "
"{input} "
"--noextract "
"--outdir {params.output} "
"&& "
"conda deactivate "
rule multiqc:
input:
expand("work/fastqc/{sample}_fastqc.zip", sample=SAMPLES)
output:
html = "report/multiqc_report.html",
params:
output = "report/"
shell:
"conda activate multiqc-1.8 "
"&& "
"multiqc "
"--no-data-dir "
"--outdir {params.output} "
"{input} "
"&& "
"conda deactivate "
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