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Add graph refinement options for pixelator 0.19 #112

Merged
merged 6 commits into from
Oct 21, 2024
Merged

Add graph refinement options for pixelator 0.19 #112

merged 6 commits into from
Oct 21, 2024

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fbdtemme
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@fbdtemme fbdtemme commented Oct 21, 2024 •
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Description

Add new graph refinement options that will come in with pixelator 0.19.

PR checklist

  • 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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/pixelator branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core 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>).
  • [] Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Oct 21, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c359165

+| ✅ 228 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-21 14:19:57

johandahlberg
johandahlberg approved these changes Oct 21, 2024
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@johandahlberg johandahlberg left a comment

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LGTM

ptajvar
ptajvar approved these changes Oct 21, 2024
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Looks good to me. I only left a small comment.

CHANGELOG.md Outdated Show resolved Hide resolved
@fbdtemme fbdtemme merged commit 95d8eed into dev Oct 21, 2024
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@fbdtemme fbdtemme deleted the feat/add-graph-refinement-options branch October 21, 2024 14:54
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@johandahlberg johandahlberg johandahlberg approved these changes

@ptajvar ptajvar ptajvar approved these changes

@ambarrio ambarrio Awaiting requested review from ambarrio

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3 participants
@fbdtemme @johandahlberg @ptajvar