Add two parameters for taxonomic classification with DADA2

d4straub commented 11 months ago

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.

Updated usage.mdto 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.

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

Closes https://github.com/nf-core/ampliseq/issues/670

PR checklist

[x] 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.
[x] Make sure your code lints (nf-core lint).
[x] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[x] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[x] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).

github-actions[bot] commented 11 months ago

`nf-core lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit d0786b7

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

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d4straub commented 11 months ago

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?

d4straub commented 11 months ago

Thanks!

nf-core / ampliseq