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Make README usage consistent with docs/usage.md #1228

Merged
merged 7 commits into from
Mar 11, 2024
Merged

Make README usage consistent with docs/usage.md #1228

merged 7 commits into from
Mar 11, 2024

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pinin4fjords
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Someone highlighted to me that this documentation is inconsistent with the usage (and in fact can create problems when using differentialabundance). Suggest a fix for consistency.

To be updated again in both places when the replacement for iGenomes is live.

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/rnaseq 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 Mar 1, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fec6d8c

+| ✅ 169 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-11 15:47:05

drpatelh
drpatelh reviewed Mar 1, 2024
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@pinin4fjords
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@nf-core-bot fix linting

@pinin4fjords
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Think we need the latest template updates to solve linting

@drpatelh
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drpatelh commented Mar 1, 2024

Yep, it appear like we didn't get an automated PR?

maxulysse
maxulysse reviewed Mar 11, 2024
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CHANGELOG.md Outdated
@@ -35,6 +35,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [PR #1241](https://github.com/nf-core/rnaseq/pull/1241) - Add nf-test tests to deseq2_qc
- [PR #1242](https://github.com/nf-core/rnaseq/pull/1242) - Use dupradar from nf-core/modules
- [PR #1244](https://github.com/nf-core/rnaseq/pull/1244) - Add gtf2bed tests
- []() - Change CI/CD testing logic to pass if no nf-tests have been ran
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😱

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That was from my cherry-picked commit (since it wasn't attached to a PR).

maxulysse
maxulysse approved these changes Mar 11, 2024
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good enough, @adamrtalbot will have to deal with merge conflicts on CHANGELOG

adamrtalbot
adamrtalbot reviewed Mar 11, 2024
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@adamrtalbot adamrtalbot mentioned this pull request Mar 11, 2024
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drpatelh
drpatelh approved these changes Mar 11, 2024
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Thanks!

@pinin4fjords pinin4fjords merged commit e6d6efe into dev Mar 11, 2024
106 checks passed
@pinin4fjords pinin4fjords deleted the readme_usage branch March 11, 2024 15:58
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@adamrtalbot adamrtalbot adamrtalbot approved these changes

@vmkalbskopf vmkalbskopf vmkalbskopf left review comments

@maxulysse maxulysse maxulysse approved these changes

@drpatelh drpatelh drpatelh approved these changes

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@pinin4fjords @drpatelh @maxulysse @adamrtalbot @vmkalbskopf