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template update 3.0.1 #629

Merged
merged 9 commits into from
Oct 11, 2024
Merged

template update 3.0.1 #629

merged 9 commits into from
Oct 11, 2024

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ramprasadn
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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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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 10, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit bb4dd58

+| ✅ 200 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.1
  • Run at 2024-10-11 08:28:35

@ramprasadn ramprasadn marked this pull request as ready for review October 10, 2024 10:04
@ramprasadn ramprasadn requested review from jemten and fellen31 October 10, 2024 10:04
jemten
jemten reviewed Oct 10, 2024
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Rapid 🚀

CITATIONS.md
@@ -50,7 +50,7 @@

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
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Should we format the other entries to not be indented?

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Good catch! I changed these back to what they were before.

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Oops that didn't work. I have changed the way we present Nextflow & nf-core's citations to align with the rest of the tools, and now it does.

assets/schema_input.json
Comment on lines +50 to +59
"oneOf": [
{
"type": "integer",
"enum": [0, 1, 2]
},
{
"type": "string",
"enum": ["other"]
}
],
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neat!

@ramprasadn ramprasadn requested a review from jemten October 11, 2024 08:46
jemten
jemten approved these changes Oct 11, 2024
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Looks good!

@ramprasadn ramprasadn merged commit 3374172 into dev Oct 11, 2024
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@ramprasadn ramprasadn deleted the template301 branch October 11, 2024 09:02
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@jemten jemten jemten approved these changes

@fellen31 fellen31 Awaiting requested review from fellen31

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@ramprasadn @jemten @nf-core-bot