A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

PR for changing `--protocol` to `--trim_primers` boolean with backward compatibility <https://github.com/nf-core/viralrecon/pull/586>

Did you review <@U043Y6FQR6J>’s comments?

Should we keep metagenomic for the test and config files

I changed file names and old references to old names

<@U043Y6FQR6J> already approved your PR magda! Make sure you have your branch updated as Maria Lara merged hers! Once everything is updated and test passes you can merge! Thanks you guys for your work!