Harshil Patel

Hi @schaffman5 ! Wondering whether you managed to fix this issue?

Closing for now but feel free to re-open if the issue persists or if you are able to update us with how you fixed it. Thanks!

Hi @riederd ! I have written up an explanation of this here: https://github.com/nf-core/viralrecon/issues/283#issuecomment-1046237471 TL;DR With the latest Nextflow DSL2 syntax we use in nf-core pipelines you can't use the `-c`...

Thank you for the detailed info @FelixKrueger ! I agree that most of these sequences won't align but I would personally prefer for these to removed at the "adapter" trimming...

Ah, I see! So it won't trim the conventional adapters if you use `args = '--fastqc -a {A}10'` in which case you would have to perform the adapter trimming twice...

Sorry, I meant running only the trimming (and other mandatory) steps first time around and then running the pipeline full blown with either `--polyA` or `-a {10}` the second time...

> you might just look at the mapping efficiency, see that it's great and move on Good point! We also do have the cutadapt logs in the MultiQC report where...

Absolutely! That would be great @BatoolMM 😎

Hi @didillysquat ! Apologies for the late response. I am holiday at the mo. It's actually required to build the decoy sequences for the [Salmon index](https://github.com/nf-core/rnaseq/blob/8094c42add6dcdf69ce54dfdec957789c37ae903/modules/nf-core/modules/salmon/index/main.nf#L31). If you have a...

Hi @didillysquat ! I was going to have a go at adding this feature for the 3.4 release but it will take quite a bit of refactoring so maybe we...