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Added module picard MeanQualityByCycle #8289

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Merged
Joon-Klaps merged 9 commits into from
Apr 24, 2025
Merged

Added module picard MeanQualityByCycle #8289

Joon-Klaps merged 9 commits into from
Apr 24, 2025

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@mikefeixu mikefeixu commented Apr 14, 2025

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.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • 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:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@mikefeixu mikefeixu requested review from anoronh4 and johnoooh April 14, 2025 00:27
@mikefeixu mikefeixu requested a review from Joon-Klaps April 23, 2025 20:42
Joon-Klaps
Joon-Klaps requested changes Apr 24, 2025
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LGTM! One thing, think it will be easier if the output channel is just pdf, to be more consistent with other modules. It's kind of nitpicking, I'm sorry 😅

@mikefeixu mikefeixu requested a review from Joon-Klaps April 24, 2025 15:51
@Joon-Klaps Joon-Klaps added this pull request to the merge queue Apr 24, 2025
Merged via the queue into nf-core:master with commit a2f12b3 Apr 24, 2025
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famosab pushed a commit to famosab/modules that referenced this pull request Jun 3, 2025
@mikefeixu @Joon-Klaps @famosab
Added module picard MeanQualityByCycle (nf-core#8289)
24d9eba 
* Added module picard MeanQualityByCycle

* Updated picard version for conda

* Code improvement per reviewer feedback.

* Update modules/nf-core/picard/meanqualitybycycle/main.nf

Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>

* Update modules/nf-core/picard/meanqualitybycycle/meta.yml

Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>

* Update modules/nf-core/picard/meanqualitybycycle/tests/main.nf.test

Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>

* Update test snap to reflect the updates from chart to pdf.

---------

Co-authored-by: “Fei <“xuf2@mskcc.org”>
Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
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@Joon-Klaps Joon-Klaps Joon-Klaps approved these changes

@anoronh4 anoronh4 Awaiting requested review from anoronh4

@johnoooh johnoooh Awaiting requested review from johnoooh

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@mikefeixu @Joon-Klaps