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Increase CPU and memory for CI because default Github runner resource doubled #76

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Increase CPU and memory for CI because default Github runner resource doubled #76

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gq1
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@gq1 gq1 commented May 3, 2024

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).

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github-actions bot commented May 3, 2024

This PR is against the main branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @gq1,

It looks like this pull-request is has been made against the sanger-tol/variantcalling main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the sanger-tol/variantcalling dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

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github-actions bot commented May 3, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b3dd6f9

+| ✅ 125 tests passed       |+
#| ❔  26 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-variantcalling_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-variantcalling_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-variantcalling_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: assets/multiqc_config.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/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.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-variantcalling_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-variantcalling_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-variantcalling_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/variantcalling/variantcalling/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2024-05-03 13:26:35

@gq1 gq1 changed the base branch from main to dev May 3, 2024 13:27
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gq1 commented May 3, 2024

@muffato
It seems increasing the resources for CI for this pipeline didn't improve anything. It took around 5mins both before and after the change.

And also this CI is not just for testing on Github, I can use it on my laptop and farm. The laptop may not have 4 cores or 10G memory and also the requirement may be wasteful on the farm.

I know some other pipelines may have CI profile just for Github, maybe we should treat this pipeline by pipeline, not just apply the changes to all of them.

@gq1 gq1 self-assigned this May 3, 2024
@gq1 gq1 requested a review from muffato May 3, 2024 13:39
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muffato commented May 3, 2024

Those are very good points. Yes, it makes sense to decide this on a pipeline-per-pipeline basis

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gq1 commented May 3, 2024

Probably I will not merge this, just close it.

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gq1 commented May 3, 2024 •
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This resource config is actually from nf-core template:
https://github.com/sanger-tol/variantcalling/blob/TEMPLATE/conf/test.config

Does the nf-core update their template? The runner updating in 17 Jan and the latest nf-core release 2.13.1 on 29th Feb.

I will check it any changes from the template.

The latest nf-core 2.13.1 didn't change the template.

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muffato commented May 3, 2024

Yes, nf-core still update the template, although perhaps not every release. Maybe they don't know about the GitHub CI Runner change either.

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muffato commented May 3, 2024

OK to close this one

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gq1 commented May 3, 2024

More resources are not necessary and this profile can be used not just in Github runnder.

@gq1 gq1 closed this May 3, 2024
@gq1 gq1 deleted the ci_resource branch May 3, 2024 18:36
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