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Add SILVA 138.2 for DADA2 #798

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merged 6 commits into from
Nov 21, 2024
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@d4straub d4straub commented Nov 15, 2024

Closes #791

I tested with nextflow run d4straub/ampliseq -r add-dada2-silva-138.2 -profile cfc,test --outdir results_add-dada2-silva-138.2 -resume --dada_ref_taxonomy silva and all seemed fine.

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/ampliseq 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).

@d4straub d4straub marked this pull request as ready for review November 15, 2024 17:22
@d4straub
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I added the SILVA 138.2 database to sbdi_compatible_databases , could you confirm that this is fine @erikrikarddaniel ?

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Sure. And if it's not it wouldn't be a big deal.

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Thanks!

@d4straub d4straub merged commit be2d1b5 into nf-core:dev Nov 21, 2024
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@d4straub d4straub deleted the add-dada2-silva-138.2 branch November 21, 2024 13:55
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3 participants