Add ATAC-Seq data support

[heylf]

Description of feature

This goes hand in hand with the issue for CITE-Seq (https://github.com/nf-core/scrnaseq/issues/99). Does it make sense to also try to integrate ATAC-Seq data support in the pipeline as well? scATAC-Seq is also supported by Cell-Ranger's 10x. I will test out the pipeline on some real data anyway in a few days.

Yet, since the name is scrnaseq, it might be a bit hard for people to notice that the pipeline can also be used for scATAC-seq data.

[grst]

I just learned this would require the cellranger-arc pipeline which seems independent of the regular cellranger command?

So we would probably want to build a separate cellranger-arc module and support this as a separate aligner ("cellranger-arc" among "cellranger"/"kallisto"/"alevin-fry")? Any other thoughts about how to best implement this?

[heylf]

I think it's the best way to go for multiome. For scATAC alone, you could use cellranger itself. I wanted to implement the cellranger-arc module and am currently working on it.

[klkeys]

For scATAC alone, you could use cellranger itself. is this still true? it seems like you need cellranger-atac, whereas cellranger-arc handles the multiome data

scATAC data support should work once https://github.com/nf-core/modules/pull/2450 is merged

[grst]

closing in favor of https://github.com/nf-core/scrnaseq/issues/174