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Switch back to scratch=false for large genomes #139

Merged
merged 5 commits into from
Sep 10, 2024
Merged

Switch back to scratch=false for large genomes #139

merged 5 commits into from
Sep 10, 2024

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muffato
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@muffato muffato commented Sep 9, 2024

Same as sanger-tol/blobtoolkit#108 for the genome-note pipeline.

Also fixed some release metadata.

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
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile 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).

@muffato muffato self-assigned this Sep 9, 2024
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github-actions bot commented Sep 9, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 878921e

+| ✅ 132 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-genomenote_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomenote_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomenote_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/igenomes.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File does not exist: assets/nf-core-genomenote_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomenote_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomenote_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/genomenote/genomenote/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2024-09-10 17:37:50

@muffato muffato changed the title Switch back to scratch=false for large genomes Switch back to scratch=false for large genomes Sep 9, 2024
@muffato muffato merged commit 2208ff8 into main Sep 10, 2024
6 checks passed
@muffato muffato deleted the patch branch September 10, 2024 19:33
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@BethYates BethYates BethYates approved these changes

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@muffato @BethYates