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Misc fixes before release #117

Merged
merged 3 commits into from
Oct 16, 2024
Merged

Misc fixes before release #117

merged 3 commits into from
Oct 16, 2024

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muffato
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@muffato muffato commented Oct 14, 2024 •
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  • Bumped up the underlying BlobToolKit software to solve a bug we faced on the Corroboree frog with @BethYates
  • Make blastn run up to the week queue but don't go in the basement queue (not needed in practice)
  • Documentation update to address number of busco databases #115

Explanation about the runtime limits for blastn: 85.9% of jobs complete within 4 hours, 98% within 47 hours, and 99.7% within 167 hours.

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>).
  • 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).

@muffato muffato requested a review from tkchafin October 14, 2024 16:19
@muffato muffato self-assigned this Oct 14, 2024
@muffato muffato mentioned this pull request Oct 14, 2024
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github-actions bot commented Oct 14, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit dfb4655

+| ✅ 128 tests passed       |+
#| ❔  29 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-blobtoolkit_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-blobtoolkit_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: CODE_OF_CONDUCT.md
  • 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/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • 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: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: assets/nf-core-blobtoolkit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/blobtoolkit/blobtoolkit/.github/workflows/awstest.yml
  • template_strings - template_strings
  • merge_markers - merge_markers

✅ Tests passed:

Run details

  • nf-core/tools version 2.11
  • Run at 2024-10-14 16:30:53

@muffato
Bumped up the underlying BTK version because 4.3.9 had a bug
abe2b76
@muffato
Updated the blastn runtime requirements to avoid basement jobs
dfb4655 
Indeed, 85.9% of jobs complete within 4 hours, 98% within 47 hours, and 99.7% within 167 hours
@tkchafin tkchafin merged commit 93bda84 into dev Oct 16, 2024
6 checks passed
@tkchafin tkchafin deleted the misc_fixes branch October 16, 2024 09:59
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@tkchafin tkchafin tkchafin approved these changes

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@muffato @tkchafin