Nick Semenkovich

Is this repository covered by a license? (e.g. MIT, etc.?)

bedtools sample is undocumented on RTD

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I didn't even know the "sample" feature existed, relying in part on this list: https://bedtools.readthedocs.io/en/latest/content/bedtools-suite.html ``` $ bedtools sample Tool: bedtools sample (aka sampleFile) Version: v2.30.0 Summary: Take sample of...

Tutorial 4 / scRNA Discovery / When to adjust Jaccard matrix p-value cutoff?

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We have a scRNA dataset where we've had difficulty discovering ecotypes with EcoTyper when using a jaccard pval cutoff of 0.05. I'm considering loosening the Jaccard p-value cutoff -- in...

Doesn't respect pipe() groups or `group:` tags & --dry-run output differs from real-world group execution

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**Snakemake version** 7.12.1 **Describe the bug** I have a Snakemake pipeline where different rules with `temp(pipe())` linking them are not run in the same group. Perplexingly, when I run snakemake...

Feature request: defining ground truths

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Thanks so much for this incredible work! I'd love to see (if you're adding features), options to define ground ground truths based on known marker genes, outside just `file_known_markers` —...

Error in GenerateColours

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When processing 11 samples, I get this error:  ``` Error in GenerateColours(num_colours = length(sample_names), names = sample_names, : GenerateColours: Cannot generate the requested number of colours. Please change palette...

This PR updates and expands the list of serial numbers of Illumina 2-color SBS sequencers for poly-g trimming. These values come from: https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000003880 This expands the previous 2-color list by...

Congrats on the paper! These are lovely tools, but the research use only restriction / noncommercial limit for .pat/.beta will likely limit adoption. Would y'all consider relicensing just that component...