KEGG warn message

[vruggieri]

Thanks for providing this nice pipeline! I run an analysis with the following command: ./nextflow run TransPi.nf --all --maxReadLen 143 --k 25,35,55,75,85 --reads '/media/server2/Data_2Gb/Melongena/Data/Trimmed/Trimmed/provaR673_HP/R673HP831val_R[1,2].fastq.gz' --outdir /media/server2/Data_2Gb/Melongena/TransPi_R673_HP8 -profile docker --skipQC

Everthing was ok, except that the pipeline ended with a KEGG warning message: "WARN: Access to undefined parameter skipKegg -- Initialise it to a default value eg. params.skipKegg = some_value" annotation. Indedd in the trinotate folder the KEGG report file is empty as well as the kegg section in the html.

Any suggestion for that issue?

Thank you in advance

[dpaz-corals]

@PalMuc did you find any solution to this issue?

[vruggieri]

Not yet. I'm still getting the same issue.

[AlexGaithuma]

try adding the option: --withkegg

in your command

./nextflow run TransPi.nf --all --maxReadLen 143 --k 25,35,55,75,85 --reads '/media/server2/Data_2Gb/Melongena/Data/Trimmed/Trimmed/provaR673_HP/R673HP831val_R[1,2].fastq.gz' --outdir /media/server2/Data_2Gb/Melongena/TransPi_R673_HP8 -profile docker --skipQC