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Manual attempt of template sync for 3.0.2 #695

Merged
merged 22 commits into from
Oct 22, 2024
Merged

Manual attempt of template sync for 3.0.2 #695

merged 22 commits into from
Oct 22, 2024

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jfy133
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@jfy133 jfy133 commented Oct 16, 2024

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/mag 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).

@jfy133 jfy133 changed the title Manual attempt of tempalte sync for 3.0.2 Manual attempt of template sync for 3.0.2 Oct 16, 2024
@jfy133 jfy133 marked this pull request as draft October 16, 2024 15:11
nvnieuwk
nvnieuwk reviewed Oct 16, 2024
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github-actions bot commented Oct 16, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0ab0f58

+| ✅ 319 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • 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
  • 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-22 06:56:51

@jfy133
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jfy133 commented Oct 17, 2024 •
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TODO:

  • Update nf-schema patch when released (will cause failures until fixed)
  • check input validation still working against broken sheets: borked.zip

@jfy133 jfy133 marked this pull request as ready for review October 21, 2024 11:44
mashehu
mashehu approved these changes Oct 21, 2024
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nextflow.config
@@ -150,7 +150,7 @@ params {
save_mmseqs_db = false

// References
genome = null
//genome = null // we use --host_genome instead
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Suggested change
//genome = null // we use --host_genome instead

or do you want to explicitly document it?

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Easier for template merges to remember to 'deactivate it'

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not anymore for future template updates thanks to the skip_features: [igenomes]

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@jfy133 jfy133 merged commit 31aceb5 into dev Oct 22, 2024
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@jfy133 jfy133 deleted the nf-core-template-merge-3.0.2-manual branch October 22, 2024 07:27
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@nvnieuwk nvnieuwk nvnieuwk left review comments

@mashehu mashehu mashehu approved these changes

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@jfy133 @mashehu @nvnieuwk @nf-core-bot