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simplify default tests + add conda/singularity #736

Merged
merged 13 commits into from
Sep 8, 2022
Merged

simplify default tests + add conda/singularity #736

merged 13 commits into from
Sep 8, 2022

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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 Sep 7, 2022 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 349e1d6

+| ✅ 151 tests passed       |+
#| ❔   4 tests were ignored |#

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.5.1
  • Run at 2022-09-08 08:32:04

FriederikeHanssen
FriederikeHanssen reviewed Sep 7, 2022
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love it, some haplotypecaller test might not work. IIRC the cnnscorevariants module doesn't run with conda, deepvariant also not

@maxulysse
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love it, some haplotypecaller test might not work. IIRC the cnnscorevariants module doesn't run with conda, deepvariant also not

Figured it'll be good at some point to have that, I'm trying things out here as usual before shipping it out in the TEMPLATE

maxulysse
maxulysse commented Sep 8, 2022
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conf/test.config
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
fixOwnership = true
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Decided to remove that instead of fixing it, as it was causing the strelkabp test to fail...

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only now?

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yes because it wasn't working, it should have been:
docker.fixOwnership = true
But when I do that, then the test fails.
So as it wasn't really working to start with, decide to remove it instead of fixing it

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ok

FriederikeHanssen
FriederikeHanssen approved these changes Sep 8, 2022
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❤️ 🎉

@maxulysse maxulysse merged commit f944d43 into nf-core:dev Sep 8, 2022
@maxulysse maxulysse deleted the dev_complete_CI branch September 8, 2022 09:33
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @FriederikeHanssen