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Fix --dada_ref_tax_custom without --dada_ref_tax_custom_sp #643

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merged 3 commits into from
Sep 29, 2023
Merged

Fix --dada_ref_tax_custom without --dada_ref_tax_custom_sp #643

merged 3 commits into from
Sep 29, 2023

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d4straub
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@d4straub d4straub commented Sep 29, 2023 •
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This is a bug fix:
nextflow run nf-core/ampliseq -r 2.5.0 -profile test_reftaxcustom,singularity --outdir results --dada_ref_tax_custom_sp false --skip_dada_addspecies
was fine but
nextflow run nf-core/ampliseq -r 2.6.1 -profile test_reftaxcustom,singularity --outdir results --dada_ref_tax_custom_sp false --skip_dada_addspecies
failed with
ERROR ~ No such variable: ch_addspecies

Obviously that function was broken after introduction, so I added a test in the new test_failed.conf that should prevent that in future.

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!
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  • 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).
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github-actions bot commented Sep 29, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9c91a4d

+| ✅ 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 2023-09-29 07:17:40

erikrikarddaniel
erikrikarddaniel approved these changes Sep 29, 2023
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👍

@d4straub d4straub changed the title Fix skip dada addspecies Fix --dada_ref_tax_custom without --dada_ref_tax_custom_sp Sep 29, 2023
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Thanks!

@d4straub d4straub merged commit 00132e7 into nf-core:dev Sep 29, 2023
17 checks passed
@d4straub d4straub deleted the fix-skip_dada_addspecies branch September 29, 2023 07:55
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

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@d4straub @erikrikarddaniel