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Pin version of nf-validation and nf-iridanext #11 #12

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merged 4 commits into from
Feb 22, 2024
Merged

Pin version of nf-validation and nf-iridanext #11 #12

merged 4 commits into from
Feb 22, 2024

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kylacochrane
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…tflow.config file

This PR is linked to the following issue: Pin version of nf-validation and nf-iridanext #11

This PR pins two Nextflow plugins to specific versions in the nextflow.config file:

  • nf-validation@1.1.3
  • nf-iridanext@0.2.0

This change was required due to an upcoming upgrade of the nf-validation plugin from 1.1.3 to 2.0.0 which will make breaking changes (nextflow-io/plugins#66).

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

apetkau
apetkau requested changes Feb 22, 2024
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This looks great to me. Thanks so much @kylacochrane 😄 . I have just one comment.

CHANGELOG.md Show resolved Hide resolved
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github-actions bot commented Feb 22, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 7740f34

+| ✅ 116 tests passed       |+
#| ❔  27 tests were ignored |#
!| ❗   2 tests had warnings |!
-| ❌   6 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/WorkflowFetchdatairidanext.groovy
  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.0.1
  • schema_lint - Schema $id should be https://github.com/phac-nml/fetchdatairidanext/master/nextflow_schema.json
    Found https://github.com/phac-nml/fetchdatairidanext/main/nextflow_schema.json

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-fetchdatairidanext_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-fetchdatairidanext_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-fetchdatairidanext_logo_dark.png
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File does not exist: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-fetchdatairidanext_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-fetchdatairidanext_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-fetchdatairidanext_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fetchdatairidanext/fetchdatairidanext/.github/workflows/awstest.yml
  • actions_awsfulltest - actions_awsfulltest
  • pipeline_name_conventions - pipeline_name_conventions

✅ Tests passed:

Run details

  • nf-core/tools version 2.13
  • Run at 2024-02-22 21:31:23

apetkau
apetkau approved these changes Feb 22, 2024
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This all looks great to me. Thanks so much @kylacochrane 🥳

The failing nf-core lint will be addressed later when we have more time to sync our pipeline with latest nf-core.

@kylacochrane kylacochrane merged commit cc8f996 into phac-nml:dev Feb 22, 2024
5 of 6 checks passed
@kylacochrane kylacochrane deleted the nf-validation-plugin-versioning branch February 22, 2024 22:36
@kylacochrane kylacochrane mentioned this pull request Feb 23, 2024
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@kylacochrane @apetkau