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Let QIIME2 accept special symbols in taxonomy strings #554

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merged 2 commits into from Mar 15, 2023
Merged

Let QIIME2 accept special symbols in taxonomy strings #554

merged 2 commits into from Mar 15, 2023

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d4straub
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@d4straub d4straub commented Mar 15, 2023 •
edited

Addresses a problem that occurs in 2.5.0 that choosing silva_132.18s.99_rep_set.dada2.fa.gz with --dada_ref_tax_custom,
i.e. with nextflow run nf-core/ampliseq -r 2.5.0 -profile singularity --input samplesheet.tsv --dada_assign_taxlevels "Eukaryota,Opisthokonta,Holozoa,Metazoa,Tetrapoda,Mammalia,Homo,Genus" --dada_ref_tax_custom "https://zenodo.org/record/1447330/files/silva_132.18s.99_rep_set.dada2.fa.gz" --skip_dada_addspecies --outdir results
the taxonomic strings contain # and ' and will fail to be transferred to QIIME2. This PR fixes the issue.

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 lint).
  • Ensure the test suite passes (nextflow run . -profile 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).

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github-actions bot commented Mar 15, 2023 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4db5f77

+| ✅ 155 tests passed       |+
#| ❔   1 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 2.7.2
  • Run at 2023-03-15 13:56:22

erikrikarddaniel
erikrikarddaniel approved these changes Mar 15, 2023
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Looks good.

@d4straub
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Thanks!

@d4straub d4straub merged commit 90eaa9c into nf-core:dev Mar 15, 2023
14 checks passed
@d4straub d4straub deleted the fix-tax-symbols branch March 15, 2023 15:52
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

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