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Check for SBDI compatibility for sintax #617

Merged
merged 8 commits into from
Aug 17, 2023
Merged

Check for SBDI compatibility for sintax #617

merged 8 commits into from
Aug 17, 2023

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jtangrot
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Fixes check for database compatibility with --sbdiexport when sintax is used. Previously, tests failed if incompatible dada2 database is given, even if sintax is used for taxonomy assignment.

PR checklist

  • This comment contains a description of changes (with reason).
  • 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 Aug 17, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0b1572f

+| ✅ 152 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 2.9
  • Run at 2023-08-17 07:22:07

d4straub
d4straub approved these changes Aug 17, 2023
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LGTM

@jtangrot
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Thanks!

@jtangrot jtangrot merged commit 0bb9caf into nf-core:dev Aug 17, 2023
@jtangrot jtangrot deleted the sbdi-compatible_sintax branch August 17, 2023 08:17
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@d4straub d4straub d4straub approved these changes

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@jtangrot @d4straub