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POC: adapt pipeline to use nf-validation - testing #1034

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POC: adapt pipeline to use nf-validation - testing #1034

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mirpedrol
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@mirpedrol mirpedrol commented May 30, 2023 •
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This PR adapts the pipeline to use nf-validation plugin for testing purposes before a template update.

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github-actions bot commented May 30, 2023 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit ae8b521

+| ✅ 142 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   4 tests had warnings |!
-| ❌   6 tests failed       |-

❌ Test failures:

  • files_exist - File not found: lib/nfcore_external_java_deps.jar
  • files_exist - File not found: lib/NfcoreSchema.groovy
  • nextflow_config - Config variable not found: params.show_hidden_params
  • nextflow_config - Config variable not found: params.schema_ignore_params
  • files_unchanged - pyproject.toml does not match the template
  • schema_params - Param validationSchemaIgnoreParams from nextflow config not found in nextflow_schema.json

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: '3.12.0'
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • 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 does not exist: lib/nfcore_external_java_deps.jar
  • files_unchanged - File ignored due to lint config: lib/NfcoreSchema.groovy
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-06-09 12:22:10

@mirpedrol mirpedrol mentioned this pull request Jun 7, 2023
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@drpatelh
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drpatelh commented Jul 6, 2023

Thanks @mirpedrol ! This has now been added in #1058

@drpatelh drpatelh closed this Jul 6, 2023
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@mirpedrol @drpatelh