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Default to 8000 UMIs as minimum component size#183

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johandahlberg merged 2 commits intodevfrom
feature/default-to-8000-as-min-component-size
Feb 12, 2026
Merged

Default to 8000 UMIs as minimum component size#183
johandahlberg merged 2 commits intodevfrom
feature/default-to-8000-as-min-component-size

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@ptajvar ptajvar commented Feb 12, 2026

We have observed from a variety of cell types that setting minimum component size to 8000 UMIs is a robust threshold for cell calling. So, we are setting that as the pipeline default value.

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  • 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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@ptajvar ptajvar requested a review from a team as a code owner February 12, 2026 08:53
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github-actions bot commented Feb 12, 2026 •
edited by nf-core-bot
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Feb 12, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 566a6d2

+| ✅ 231 tests passed       |+
#| ❔   8 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   4 tests had warnings |!
Details

❗ Test warnings:

  • files_unchanged - LICENSE does not match the template
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-02-12 12:11:34

@ptajvar ptajvar changed the base branch from master to dev February 12, 2026 10:05
@ptajvar ptajvar force-pushed the feature/default-to-8000-as-min-component-size branch from 0d939b1 to a9daeea Compare February 12, 2026 10:08
johandahlberg
johandahlberg approved these changes Feb 12, 2026
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Could you write a line about this in the changelog as well? Then we can go ahead and merge this.

@johandahlberg johandahlberg merged commit 7094800 into dev Feb 12, 2026
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@Aratz Aratz mentioned this pull request Feb 26, 2026
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@johandahlberg johandahlberg johandahlberg approved these changes

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@ptajvar @johandahlberg