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Remove concatenate_vcfs tests with singularity #1039

Merged
merged 2 commits into from
May 25, 2023
Merged

Remove concatenate_vcfs tests with singularity #1039

merged 2 commits into from
May 25, 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).

@maxulysse
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close #1037

@FriederikeHanssen
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https://nfcore.slack.com/archives/C03EZ806PFT/p1680092451410239

@FriederikeHanssen
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Can you add them to the manual tests? And why is there only not enough space with singularity?

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github-actions bot commented May 25, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit cc29ea3

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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-05-25 10:50:01

@maxulysse
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Can you add them to the manual tests?

The tests are still run, just not with singularity, so they'll be launch when tried locally on singularity

And why is there only not enough space with singularity?

I'm assuming since singularity doesn't do layers, there are a lot of duplication, and this test was using a lot of variant callers.

@FriederikeHanssen FriederikeHanssen merged commit 9b933a1 into nf-core:dev May 25, 2023
@maxulysse maxulysse deleted the concatenate_singularity branch May 25, 2023 11:56
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@nvnieuwk nvnieuwk nvnieuwk approved these changes

@ramprasadn ramprasadn ramprasadn approved these changes

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@maxulysse @FriederikeHanssen @ramprasadn @nvnieuwk