modkit.Summary, deprecated modkit.Pileup's bedgraph option

[hexylena]

Checklist

• Pull request details were added to CHANGELOG.md.
• Documentation was updated (if required).
• parameter_meta was added/updated (if required).
• Submodule branches are on develop or a tagged commit.
• split by strand + methylation call into separate files

I was running the subsequent steps to @rhpvorderman's https://github.com/biowdl/long-read-variant-calling and encountered two steps, one that needed the bed, and one that needed the bedgraph. While looking into how I could get both outputs without running modkit pileup twce, I encountered the following issue

nanoporetech/modkit#210 (comment) and then subsequently nanoporetech/modkit#158 (comment)

This also adds support for modkit summary while I was at it.

[rhpvorderman]

Looks good. Can you check the linting? It notes that the paramater_meta now contains an input that is no longer present.

EDIT: Did it myself to get this merged.

[hexylena]

I think this should work, but I haven't tested this locally yet, maybe we should write per-task tests at some point? I'll test it soon, maybe tomorrow, and if it's successful, then I'll give an indication.

[hexylena]

$ wc -l ...
   860750 analysis/90_hg38.pseudoepic.bedgraph
   430879 analysis/90_hg38.pseudoepic.bedgraph_C_+.bedGraph
   429871 analysis/90_hg38.pseudoepic.bedgraph_C_-.bedGraph

ja dat werkt prima