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handle multiple DOIs #1496

Merged
merged 5 commits into from
May 3, 2024
Merged

handle multiple DOIs #1496

merged 5 commits into from
May 3, 2024

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maxulysse
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Replace half of #1494

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/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test tests/ --verbose --profile +docker).
  • 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 May 2, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 28e6b22

+| ✅ 181 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • 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!

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/WorkflowSarek.groovy
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-05-03 11:13:36

@maxulysse
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waiting on nf-core/modules#5556 as well

@maxulysse maxulysse mentioned this pull request May 2, 2024
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@maxulysse maxulysse changed the title handle multiple DOI handle multiple DOIs May 2, 2024
jasmezz
jasmezz previously approved these changes May 3, 2024
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@jasmezz jasmezz left a comment

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LGTM from what I understand from the string-replacing syntax. If you prefer a really close check of those lines in the main.nf, you should wait for another review. But comparing those to the nf-core subworkflow update and your changed code, it looks alright to me ;)

subworkflows/local/utils_nfcore_sarek_pipeline/main.nf Outdated Show resolved Hide resolved
@maxulysse @jasmezz
Update subworkflows/local/utils_nfcore_sarek_pipeline/main.nf
28e6b22 
Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com>
@maxulysse maxulysse merged commit 1eae2e3 into nf-core:dev May 3, 2024
22 checks passed
@maxulysse maxulysse deleted the multiple_DOI branch May 3, 2024 11:37
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@jasmezz jasmezz jasmezz approved these changes

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

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