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remove exit strategy for MANTA/STRELKA #882

Merged
merged 8 commits into from
Jun 2, 2023
Merged

remove exit strategy for MANTA/STRELKA #882

merged 8 commits into from
Jun 2, 2023

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maxulysse
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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 (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 Dec 6, 2022 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 313480b

+| ✅ 153 tests passed       |+
#| ❔   9 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-06-01 16:50:22

@FriederikeHanssen
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The exit strategy 1 should stay

@maxulysse
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The exit strategy 1 should stay

It messes up global reassignments.
But I can see why we want that to stay, but it need to go too...
Need to find a way...

@FriederikeHanssen
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is there a way to make it additive? errorStartegy += ?

@maxulysse
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The exit strategy 1 should stay

It messes up global reassignments. But I can see why we want that to stay, but it need to go too... Need to find a way...

I'll try, but not sure at all.
Anyhow, what do you think about removing most of the withName label selectors from base.config and add that in nf-core config in the awsbatch profile. Is that the one we use for the aws megatests?

This was referenced Jun 1, 2023
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@maxulysse maxulysse merged commit 78b47df into dev Jun 2, 2023
@maxulysse maxulysse deleted the maxulysse-patch-1 branch June 2, 2023 07:10
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@adamrtalbot adamrtalbot adamrtalbot approved these changes

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @FriederikeHanssen @adamrtalbot