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Use nf-validation plugin for parameter and samplesheet validation #1058

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Merged
drpatelh merged 8 commits into from
Jul 12, 2023
Merged

Use nf-validation plugin for parameter and samplesheet validation #1058

drpatelh merged 8 commits into from
Jul 12, 2023

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@drpatelh
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@drpatelh drpatelh commented Jul 6, 2023 •
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  • Strip out parameter validation now performed with nf-validation
  • Replace custom Python validation script for samplesheet with nf-validation plugin / minimal Groovy function

@drpatelh drpatelh mentioned this pull request Jul 6, 2023
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github-actions bot commented Jul 6, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8d9ccac

+| ✅ 143 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred 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 ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-10 22:36:22

nvnieuwk
nvnieuwk reviewed Jul 7, 2023
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This looks very good!

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drpatelh commented Jul 10, 2023

@nf-core-bot fix linting

nvnieuwk
nvnieuwk approved these changes Jul 12, 2023
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LGTM

@mirpedrol mirpedrol mentioned this pull request Jul 12, 2023
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@drpatelh drpatelh merged commit c6bfe7a into nf-core:dev Jul 12, 2023
@mirpedrol mirpedrol mentioned this pull request Aug 10, 2023
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@drpatelh drpatelh deleted the updates branch October 11, 2023 20:43
@pinin4fjords pinin4fjords mentioned this pull request Nov 8, 2023
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