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Improve validation of run_accessions IDs within sample IDs #484

Merged
merged 4 commits into from
May 16, 2024
Merged

Improve validation of run_accessions IDs within sample IDs #484

merged 4 commits into from
May 16, 2024

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jfy133
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@jfy133 jfy133 commented May 8, 2024

Should hopefully close #483

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/taxprofiler branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
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github-actions bot commented May 8, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c66dc4e

+| ✅ 258 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-16 10:59:19

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jfy133 commented May 8, 2024

@nf-core-bot fix linting

@sofstam sofstam self-requested a review May 8, 2024 20:48
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sofstam reviewed May 8, 2024
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Tested and it detects if a run_accession and a sample Id are not unique.

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I'm just wondering, are there good cases for when a run accession should not be globally unique, but only within a sample?

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jfy133 commented May 16, 2024

Tested and it detects if a run_accession and a sample Id are not unique.

Do you approve then @sofstam ?

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jfy133 commented May 16, 2024

I'm just wondering, are there good cases for when a run accession should not be globally unique, but only within a sample?

Depends on naming schemes basically... My definition of a run was based on ENA run accessions where they were were unique. But @sofstam had an issue where they were not unique, as they were interpreted as a sequencing run accession (so in the table, the same sequencing run was shared across all the samples).

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sofstam commented May 16, 2024

I approve, shall but shall we merge the template first?

@sofstam sofstam self-requested a review May 16, 2024 07:38
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The linting should be fixed before merging!

@jfy133 jfy133 merged commit c1e643f into dev May 16, 2024
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@jfy133 jfy133 deleted the improve-validation branch May 16, 2024 11:46
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@jfy133 @Midnighter @sofstam @nf-core-bot