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Add two parameters for taxonomic classification with DADA2 #681

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merged 1 commit into from
Dec 20, 2023
Merged

Add two parameters for taxonomic classification with DADA2 #681

merged 1 commit into from
Dec 20, 2023

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d4straub
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@d4straub d4straub commented Dec 19, 2023 •
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  1. Added two parameters:
  • --dada_addspecies_allowmultiple: Defines the behavior when multiple exact matches against different species are returned. By default only unambiguous identifications are returned. If TRUE, a concatenated string of all exactly matched species is returned.
  • --dada_taxonomy_rc: Reverse-complement of each sequences will be used for classification if it is a better match to the reference sequences than the forward sequence.
  1. Updated usage.md to explain that --dada_taxonomy_rc is recommended with --dada_ref_taxonomy gtdb according to https://zenodo.org/records/4735821:

Another concern that was raised was the orientation of the DB sequences, to get past this problem please use the tryRC = TRUE argument in the assignTaxonomy command within DADA2, this will search your ASVs in the reverse complement as well.

  1. Updated the default of --kraken2_confidence because it was always showing up as changed even if it was default.

Closes #670

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  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
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github-actions bot commented Dec 19, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d0786b7

+| ✅ 154 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-12-19 14:05:27

@d4straub
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Hi @erikrikarddaniel , I added here a parameter to allow multiple exact matches, I could not see anywhere trouble. However, could there be any consequences to SBDI?

erikrikarddaniel
erikrikarddaniel approved these changes Dec 19, 2023
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👍
Since the default is to keep the old behaviour, I can't see any problem with this.

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Thanks!

@d4straub d4straub merged commit 71ee3c1 into nf-core:dev Dec 20, 2023
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@d4straub d4straub deleted the add-dada_addspecies_allowmultiple-dada_taxonomy_rc branch December 20, 2023 07:15
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@d4straub @erikrikarddaniel