Sarai Varona

# Issue update with test dataset: ### Description of the bug When I run the pipeline with the param --skip_asciigenome in metagenomic mode with ivar variant caller, variant calling steps...

> Superb work, I'm not a super fan of the name for this new params: `--additional_annot` Why not `--additional_annotation`, it's not that much longer. Done! :heavy_check_mark:

@drpatelh @maxulysse is this issue solved? Which was the sample you were testing this with?

@Alex-Vasile @mgaucoin @Moslemecoh can we close this issue as it seems to be an ivar issue and not a viralrecon issue?

viralrecon generates the .vcf file of that .tsv that is correctly formatted. As viralrecon does not use `ivar filtervariants`, I think it is something that iVar should get fixed, and...

There is nothing to apology for! Hope this helps others to get to the problem! 😄

> We should only pass files to modules within a channel. I'd recommend to patch the modules upstream and keep this adapter input in cutadapt Thanks a lot @maxulysse! Just...

@asanenjoy could you provide us the command you used to run viralrecon and the `.nextflow.log` file?

Unless you specify something different, viralrecon will use each process default environment/image/container. So in the case of `viralrecon/modules/local/plot_mosdepth_regions.nf`: ``` process PLOT_MOSDEPTH_REGIONS { label 'process_medium' conda "conda-forge::r-base=4.0.3 conda-forge::r-reshape2=1.4.4 conda-forge::r-optparse=1.6.6 conda-forge::r-ggplot2=3.3.3 conda-forge::r-scales=1.1.1...

Sorry for the late reply @alethomas ! We will have a closer look to this to see what happens, but a workaround we do for the CI tests is downloading...