Snakefile "ymp/rules/multiqc.rules"
Env(name="multiqc", base="bioconda", packages=[
"multiqc >=1.4"
])
with Stage("qc_multiqc") as S:
S.doc("""
Aggregate QC reports using MultiQC
""")
rule multiqc_fastqc:
"""Assemble report on all FQ files in a directory"""
message:
"Aggregating QC reports for {params.pdir}"
input:
fastqc = "{:prev:}/{:fq_names:}_fastqc.zip"
output:
flist = "{:this:}/file_list.txt",
report = "{:this:}/multiqc_report.html",
log:
"{:this:}/multiqc.log"
params:
pdir = "{:prev:}"
threads:
1
conda:
"multiqc"
shell: """
echo {input.fastqc} | tr ' ' '\n' > {output.flist}
multiqc \
--verbose \
--module fastqc \
--file-list {output.flist} \
--filename {output.report} \
--title {params.pdir} \
--force \
> {log} 2>&1
cp {output.report} {output.report2}
"""