Error during Freyja aggregate step and turning off processes

[vitu1]

Hi Erin,

I'm running the latest Cecret version 3.22.24346 and running into an error on the Freyja aggregate step. It looks like the step is unable to find some of the input files or they may be mislabeled. I've attached the relevant output and log files here.

On a separate note, it looks like setting the flags for certain processes isn't turning them off. For example, I have 'fastqc', 'samtools_ampliconstats', and 'samtools_plot_ampliconstats' set to false in my config file, but it looks like they are still running

Thank you for your help!

screen.log

nextflow.log

[erinyoung]

That does look weird!!!

Let me look into it.

[erinyoung]

My apologies on this!!!

I made some changes with this PR here that should address this issue: #397

Once the changes pass all the tests, a new version will get get released that can be used.

[erinyoung]

https://github.com/UPHL-BioNGS/Cecret/releases/tag/3.25.24348 is out now! Let me know if you run into any other issues!

[vitu1]

The freyja aggregate error has been fixed with the latest update

It looks like I still can't turn off certain processes such as fastqc, bcftools_variants, samtools_plot_ampliconstats, etc. with their respective params set to false. This isn't a huge deal since the pipeline runs to completion. But just letting you know in case you want to look into it