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Update maxRetries #86

Merged
merged 2 commits into from
Oct 19, 2023
Merged

Update maxRetries #86

merged 2 commits into from
Oct 19, 2023

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priyanka-surana
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Increasing the maxRetries wrt changes in the sanger.config

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 Oct 19, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ebf0747

+| ✅ 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 2023-10-19 13:51:09

@DLBPointon
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What's the likely hood that process_high_memory processes will need 5 retries? If it does go through and ends up trying to request 1tb of mem, that will cause issues won't it? Especially as the sanger.profile caps out at 680.

Does COOLER need 200gb anyway? We get away with 100 for almost everything and even that is too large as a starting point.

@priyanka-surana
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What's the likely hood that process_high_memory processes will need 5 retries? If it does go through and ends up trying to request 1tb of mem, that will cause issues won't it? Especially as the sanger.profile caps out at 680.

This feature is generally only used by fastK and sort. Jobs that exceed the max.mem in sanger.config will get capped. And if they fail with max.mem, you are right they will get repeated with similar resources.

Does COOLER need 200gb anyway? We get away with 100 for almost everything and even that is too large as a starting point.

Honestly, we have not started analysing our log data. Currently it is assigning, 72GB (label: high) but I can reduce it further.

@priyanka-surana
Update cooler base settings
ebf0747 
Trying it out directly in GitHub 😱
@DLBPointon DLBPointon self-requested a review October 19, 2023 14:37
DLBPointon
DLBPointon approved these changes Oct 19, 2023
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LGTM!

@priyanka-surana priyanka-surana merged commit 3a60381 into dev Oct 19, 2023
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@priyanka-surana priyanka-surana deleted the maxRetries branch October 19, 2023 14:39
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@priyanka-surana @DLBPointon