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Adding new nf-core subworkflow freyja for weighted variant analysis #375

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merged 20 commits into from
Aug 16, 2023
Merged

Adding new nf-core subworkflow freyja for weighted variant analysis #375

merged 20 commits into from
Aug 16, 2023

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Joon-Klaps
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@Joon-Klaps Joon-Klaps commented Mar 29, 2023 •
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PR checklist

Closes #299
The Freyja tool, is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset, i.e. wastewater.

  • 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
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile 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).

@Joon-Klaps Joon-Klaps added enhancement Improvement for existing functionality subworkflows labels Mar 29, 2023
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github-actions bot commented Mar 29, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8c74f8f

+| ✅ 148 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: lib/WorkflowViralrecon.groovy
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-08-16 11:44:48

@Joon-Klaps Joon-Klaps changed the title installing freyja using nf-core Adding new nf-core subworkflow freyja for weighted variant analysis Mar 29, 2023
@Joon-Klaps Joon-Klaps self-assigned this Apr 3, 2023
@Joon-Klaps Joon-Klaps mentioned this pull request Apr 13, 2023
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Submitting a PR for the MultiQC module so it can be implemented in the final report:
MultiQC/MultiQC#1903

@Joon-Klaps Joon-Klaps marked this pull request as ready for review May 6, 2023 15:30
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The core functionalities for Freyja are implemented in this PR. The Multiqc module of Freyja is not yet available but a PR has been made MultiQC/MultiQC#1903. I'll make a new PR when the version of Multiqc is released that contains the Freyja module.

maxulysse
maxulysse reviewed Aug 16, 2023
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maxulysse reviewed Aug 16, 2023
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drpatelh reviewed Aug 16, 2023
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Looks awesome! Thanks @Joon-Klaps 😍 Pushed a couple of commits updating a few things.

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drpatelh
drpatelh approved these changes Aug 16, 2023
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🚀

@drpatelh drpatelh merged commit 23e3441 into nf-core:dev Aug 16, 2023
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@Joon-Klaps Joon-Klaps deleted the freyja branch August 16, 2023 12:47
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@drpatelh drpatelh drpatelh approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse

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@Joon-Klaps Joon-Klaps

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@Joon-Klaps @maxulysse @drpatelh