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Added multi chimera steps. porechop, vsearch and blast methods. - #38

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chimera
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Added multi chimera steps. porechop, vsearch and blast methods. #38
chriswyatt1 wants to merge 1 commit into
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chimera

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@chriswyatt1

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All are optional. I ran the pipeline with all options separately, and they all perform as expected.

We still need a good test dataset to make sure the chimeras as truly detected, and not filtering "good" reads.

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/nanoporemetabarcoding branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines 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).

@chriswyatt1

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For the blast step, it looks for similar hits between the two halves. Searches the top 10 blast hits by default, and checks if they correspond. There is a way to set the number of top blast hits to check.

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