I got the results like below

[@login006 mutect]$ cd cnv/

[@login006 cnv]$ ls

multiqc pipeline_info reference

[@login006 cnv]$ cd reference/

[@login006 reference]$ ls

cnvkit

[@login006 reference]$ cd cnvkit/

[@login006 cnvkit]$ ls

sampl1.antitargetcoverage.cnn sample1.targetcoverage.cnn sample2.antitargetcoverage.cnn sample2.targetcoverage.cnn panel.cnn

I want to run CNVkit within sarek pipeline on seven tumours (no match normal available) so in this code where shall I use the panel of normals I have made by two normal samples? Thanks for any help

nextflow run nf-core/sarek \

--input sample.csv \

--outdir results \

--genome GATK.GRCh38 \

--tools cnvkit \

-profile crick \

-r 3.4.2 \

-resume

https://nf-co.re/sarek/3.4.4/parameters/#cnvkit_reference (you need to press

show hidden

on the right hand side

Thanks, so shall I put

--cnvkit_reference

to

panel.cnn

if I am not wrong?