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Add multisearch with probability of overlap calculation #5

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merged 27 commits into from
Oct 18, 2024

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@olgabot olgabot commented Oct 1, 2024

Use the probability of overlap calculation provided in sourmash-bio/sourmash_plugin_branchwater#458 to compute statistical significance of search results from all-by-all comparisons.

  • Add multisearch module
  • Increas split size for split2 so it doesn't run
  • Create search subworkflow
  • Add search workflow import
  • Add versions of search output

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
  • If necessary, also make a PR on the nf-core/kmerseek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

@olgabot olgabot changed the base branch from main to dev October 1, 2024 22:11
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olgabot commented Oct 18, 2024

Filed a bug #8 re needing to update to the template in a separate PR.

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olgabot commented Oct 18, 2024

Merging and ignoring the linting issues for now

@olgabot olgabot merged commit 6c8940c into dev Oct 18, 2024
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