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fix(schema): add some params to validationSchemaIgnoreParams for better handling #1471

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merged 2 commits into from
Apr 18, 2024
Merged

fix(schema): add some params to validationSchemaIgnoreParams for better handling #1471

merged 2 commits into from
Apr 18, 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).

FriederikeHanssen
FriederikeHanssen reviewed Apr 18, 2024
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nextflow.config
@@ -97,7 +97,7 @@ params {
vep_out_format = "vcf"
vep_spliceai = null // spliceai plugin disabled within VEP
vep_spliceregion = null // spliceregion plugin disabled within VEP
vep_version = "110.0-0" // Should be updated when we update VEP, needs this to get full path to some plugins
vep_version = "111.0-0" // Should be updated when we update VEP, needs this to get full path to some plugins
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and a sneaky version update

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Changelog?

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yeah, I noticed I forgot about it while I was modifying the schema/config

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CHANGELOG updated

@maxulysse
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will close #1454

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github-actions bot commented Apr 18, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7dd75ca

+| ✅ 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 2024-04-18 12:54:31

@asp8200
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asp8200 commented Apr 18, 2024

What about the snpeff_db thing that Tower was complaining about? It that also fixed by this PR?

@maxulysse
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What about the snpeff_db thing that Tower was complaining about? It that also fixed by this PR?

yeah, that's the initial point of this PR.

@maxulysse maxulysse merged commit 5f7cf6b into nf-core:dev Apr 18, 2024
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@maxulysse maxulysse deleted the schema branch April 18, 2024 13:29
@FriederikeHanssen FriederikeHanssen mentioned this pull request Jul 8, 2024
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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3 participants
@maxulysse @asp8200 @FriederikeHanssen