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Add new denoise methods#212

Merged
Aratz merged 12 commits into
devfrom
dev-target-4.1
May 28, 2026
Merged

Add new denoise methods#212
Aratz merged 12 commits into
devfrom
dev-target-4.1

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@johandahlberg

@johandahlberg johandahlberg commented May 27, 2026 •
edited by Aratz
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This PR does the following:

  • Update pixelator to 0.27.1
  • Add ACE and PLS denoising
  • Turn off K1 denoising by default
  • Denoise before sample calling

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.

@github-actions

github-actions Bot commented May 27, 2026

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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 @johandahlberg,

It looks like this pull-request is has been made against the nf-core/pixelator 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 nf-core/pixelator 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!

@johandahlberg johandahlberg changed the base branch from master to dev May 27, 2026 14:09
@github-actions

github-actions Bot commented May 27, 2026 •
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nf-core pipelines lint overall result: Passed ✅

Posted for pipeline commit 9a6baf8

+| ✅ 231 tests passed       |+
#| ❔   9 tests were ignored |#
Details

❔ Tests ignored:

  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_exist - File is ignored: tests/default.nf.test
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-pixelator_logo_light.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-05-28 07:34:48

@Aratz Aratz force-pushed the dev-target-4.1 branch from 22fa715 to 4409f35 Compare May 28, 2026 07:28
@Aratz Aratz changed the title Dev target 4.1 Add new denoise methods May 28, 2026
@Aratz Aratz marked this pull request as ready for review May 28, 2026 07:48
@Aratz Aratz requested a review from a team as a code owner May 28, 2026 07:48
@Aratz Aratz merged commit d889bbc into dev May 28, 2026
21 checks passed
This was referenced May 28, 2026
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@Aratz Aratz Aratz approved these changes

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@johandahlberg @Aratz