modkit.Summary, deprecated modkit.Pileup's bedgraph option
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Contributor
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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. |
Contributor
Author
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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. |
Contributor
Author
ja dat werkt prima |
modkit.Pileup's bedgraph option, produce it by defaultmodkit.Summary, deprecated modkit.Pileup's bedgraph option
More reasonable bounds
DavyCats
approved these changes
Jun 2, 2025
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Checklist
parameter_metawas added/updated (if required).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 pileuptwce, I encountered the following issuenanoporetech/modkit#210 (comment) and then subsequently nanoporetech/modkit#158 (comment)
This also adds support for modkit summary while I was at it.