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Update multiqc & add freyja to MQC #413

Merged
merged 8 commits into from
Jan 25, 2024
Merged

Update multiqc & add freyja to MQC #413

merged 8 commits into from
Jan 25, 2024

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Joon-Klaps
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PR checklist

Multiqc supports the output of Freyja demix, it can be added to the pipeline.

  • 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/viralrecon 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>).
  • 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
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The result from nextflow run . -profile docker,test --outdir testing looks like this.
image

@Joon-Klaps Joon-Klaps mentioned this pull request Jan 17, 2024
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github-actions bot commented Jan 17, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 33e7256

+| ✅ 150 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   5 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 preferred methods description, e.g. add publication citation for this pipeline
  • system_exit - System.exit in nanopore.nf: System.exit(1) [line 237]

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-25 15:27:49

@Joon-Klaps
Declare empty freyja_mqc channel
f0ecb40 
don't pubslih freyja update version
@Joon-Klaps
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@nf-core-bot fix linting

@svarona
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svarona commented Jan 25, 2024

The result from nextflow run . -profile docker,test --outdir testing looks like this. image

Maybe you can add the freyja's MQC plot to the output.md file for both nanopore and Illumina, it would be great!

@svarona
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svarona commented Jan 25, 2024

Thanks a lot for these enhancements!

@Joon-Klaps Joon-Klaps merged commit d915206 into dev Jan 25, 2024
24 checks passed
@Joon-Klaps Joon-Klaps deleted the update-multiqc-freyja branch January 25, 2024 16:13
@svarona svarona mentioned this pull request Jun 11, 2024
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@svarona svarona svarona approved these changes

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@Joon-Klaps @svarona @nf-core-bot