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Kmer count + Dimensionality reduction #40

Merged
merged 97 commits into from
Apr 4, 2024
Merged

Kmer count + Dimensionality reduction #40

merged 97 commits into from
Apr 4, 2024

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weaglesBio
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

This get_kmers_profile is running the kmer count, then the selected dimensionality methods in parallel and the combining the embeddings.csv to output.

Eerik, it would be helpful if you could verify python script behaviour is correct.

@DLBPointon DLBPointon self-assigned this Mar 1, 2024
@DLBPointon DLBPointon removed the request for review from yumisims March 1, 2024 17:04
@DLBPointon DLBPointon self-requested a review April 4, 2024 12:05
@DLBPointon DLBPointon merged commit bf80071 into dev Apr 4, 2024
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@DLBPointon DLBPointon deleted the kmer_count branch April 4, 2024 13:27
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Layer 2 - Kmer Counting + dim reduction
4 participants