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Merged
sainsachiko merged 9 commits into from
Dec 1, 2025
Merged

Add module PBMARKDUP #9457

sainsachiko merged 9 commits into from
Dec 1, 2025
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@sainsachiko sainsachiko commented Nov 25, 2025 •
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Add pbmarkdup to identifies and marks duplicate reads in PacBio HiFi (CCS) data.
#9456
Thank you for reviewing!

PR checklist

Closes #XXX

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
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  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
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      • nf-core modules test <MODULE> --profile singularity
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      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
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@muffato muffato removed their request for review November 26, 2025 10:17
@sainsachiko sainsachiko requested a review from mashehu November 26, 2025 11:06
DLBPointon
DLBPointon reviewed Nov 26, 2025
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làm tốt lắm!

I just have a few comments to flesh it out more.

It'll mean adding another test, sorry. Feel free to get another opinion though.

sainsachiko
sainsachiko commented Dec 1, 2025
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DLBPointon
DLBPointon approved these changes Dec 1, 2025
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LGTM

@sainsachiko sainsachiko added this pull request to the merge queue Dec 1, 2025
Merged via the queue into nf-core:master with commit c984ada Dec 1, 2025
383 of 399 checks passed
vagkaratzas pushed a commit that referenced this pull request Dec 8, 2025
@sainsachiko @vagkaratzas
Add module PBMARKDUP (#9457)
a03e263 
* Add module pbmarkdup

* Fix linting

* Update path to test data

* Update with code review (--dup-file, log, check file name collisions)

* Fix linting

* Update path to test data

* Update modules/nf-core/pbmarkdup/meta.yml

* Fix linting
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@DLBPointon DLBPointon DLBPointon approved these changes

@mashehu mashehu Awaiting requested review from mashehu

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@sainsachiko @DLBPointon