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

nf-core

Hey, all
I was running mag pipeline on my shotgun data, using trimmomatic as clipping tool, but i was wondering there is no option for adapter removal while using trimmomatic.
modules/trimmomatic/main.nf` correctly supports `ext.args` (ILLUMINACLIP) + `ext.args2` (quality trimming)
But there is no params like `trimmomatic_adapters`, `trimmomatic_clip_r1`, etc.
- I override via custom config:
```
withName: 'TRIMMOMATIC' {
    ext.args = 'ILLUMINACLIP:NexteraPE-PE.fa:2:30:10'
}
and now its working.

You mean there is no way to specify the specific adapters?

No, that particular parameter is not directly supported at the moment but it , but it would be good thing to add! Coudl you make an issue?