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Validate umi_read_structure #2071

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Merged
FriederikeHanssen merged 5 commits into from
Dec 11, 2025
Merged

Validate umi_read_structure #2071

FriederikeHanssen merged 5 commits into from
Dec 11, 2025
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@sminot
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@sminot sminot commented Dec 8, 2025

Addresses #2068

While I have not gone through the checklist, since this is a one-line change I was hoping it would be uncontroversial.

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github-actions bot commented Dec 8, 2025

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @sminot,

It looks like this pull-request is has been made against the sminot/sarek master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the sminot/sarek dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@sminot sminot changed the base branch from master to dev December 8, 2025 22:46
@SPPearce
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SPPearce commented Dec 9, 2025

Ah, that is my bad.
Failing tests are sentieon by the looks of it.

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SPPearce commented Dec 9, 2025

Can you update the changelog please

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sminot commented Dec 9, 2025

Can you update the changelog please

Of course, and thank you!

SPPearce
SPPearce reviewed Dec 9, 2025
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CHANGELOG.md Outdated

### Added

- [#2071](https://github.com/nf-core/sarek/pull/2071) - Updated parameter validation to support the use of umi_read_structure along with umi_in_read_headers
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@SPPearce SPPearce Dec 9, 2025

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I think this should be under Fixed rather than Added.

SPPearce
SPPearce approved these changes Dec 10, 2025
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The test failures are from the sentieon tests as far as I can see.

FriederikeHanssen
FriederikeHanssen reviewed Dec 10, 2025
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CHANGELOG.md

### Fixed

- [#2071](https://github.com/nf-core/sarek/pull/2071) - Updated parameter validation to support the use of umi_read_structure along with umi_in_read_headers
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@FriederikeHanssen FriederikeHanssen Dec 10, 2025

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I think this needs ot be moved to the dev section of the changelog

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@FriederikeHanssen FriederikeHanssen Dec 10, 2025

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like just up, because we had a release in the meantime

@sminot sminot enabled auto-merge December 10, 2025 16:53
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FriederikeHanssen commented Dec 11, 2025

@sminot can you merge in dev and fix the changelog please?

@FriederikeHanssen FriederikeHanssen merged commit 4c2ef41 into nf-core:dev Dec 11, 2025
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@FriederikeHanssen FriederikeHanssen mentioned this pull request Dec 11, 2025
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SPPearce commented Dec 12, 2025

Thanks @sminot and @FriederikeHanssen

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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@SPPearce SPPearce SPPearce approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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3 participants

@sminot @SPPearce @FriederikeHanssen