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fix(CI): add spark profile to all spark tests #1463

Merged
merged 3 commits into from
Apr 13, 2024
Merged

fix(CI): add spark profile to all spark tests #1463

merged 3 commits into from
Apr 13, 2024

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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 maxulysse marked this pull request as ready for review April 13, 2024 09:15
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github-actions bot commented Apr 13, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5659d3d

+| ✅ 180 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.4.1
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/WorkflowSarek.groovy
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • 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: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-13 09:20:03

FriederikeHanssen
FriederikeHanssen reviewed Apr 13, 2024
View reviewed changes
tests/test_gatk4spark.yml
@@ -49,7 +49,7 @@
- path: results/preprocessing/mapped/
should_exist: false
- name: Run default pipeline with gatk4spark and skipping all QC steps
command: nextflow run main.nf -profile test_cache,use_gatk_spark --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools --outdir results
command: nextflow run main.nf -profile test_cache,use_gatk_spark,spark --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools --outdir results
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I missed a bunch of discussion around this. What is tl;dr that we have a double spark profile?

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So 1 for the test, and one for the docker.userEmulation that restore proper usage

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ah makes sense, so users should set spark when runnin it now?

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Yes, I think that was the cleanest option I could think of. And if people need, they can use a custom config easily

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makes sense :)

@maxulysse maxulysse merged commit 63bc017 into nf-core:dev Apr 13, 2024
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @FriederikeHanssen