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Fix: Cloud Storage objects are immutable on GCP #1494

Merged
merged 11 commits into from
May 3, 2024
Merged

Fix: Cloud Storage objects are immutable on GCP #1494

merged 11 commits into from
May 3, 2024

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maxulysse
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Most likely culprit is the sort: false in the collectFile()

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 5ab5292

+| ✅ 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 13:31:20

@maxulysse maxulysse changed the title Fix Cloud Storage objects are immutable Fix: Cloud Storage objects are immutable on GCP + multiple doi handling May 2, 2024
@asp8200
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asp8200 commented May 2, 2024 •
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I guess this should fix this, right?

Has the proposed solution been tested on GCP?

@maxulysse maxulysse mentioned this pull request May 2, 2024
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FriederikeHanssen
FriederikeHanssen previously approved these changes May 2, 2024
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I'll approve, but I think we should get Esha's ok here.

@maxulysse
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maxulysse commented May 2, 2024 •
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cf nf-core/tools#2947

@maxulysse
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sorry for fixing two issues in 1 PR, but I encountered the second issue while fixing the first one

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splitting the DOI thingy in another PR as it's becoming to be a bigger part of the PR

@maxulysse maxulysse mentioned this pull request May 2, 2024
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@maxulysse maxulysse changed the title Fix: Cloud Storage objects are immutable on GCP + multiple doi handling Fix: Cloud Storage objects are immutable on GCP May 2, 2024
@maxulysse maxulysse merged commit 67914f8 into nf-core:dev May 3, 2024
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@FriederikeHanssen FriederikeHanssen mentioned this pull request Jul 8, 2024
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@SPPearce SPPearce SPPearce approved these changes

@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

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@maxulysse @asp8200 @FriederikeHanssen @SPPearce