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Use nf-validation plugin for parameter and samplesheet validation #112

Merged
merged 8 commits into from
Jul 24, 2023
Merged

Use nf-validation plugin for parameter and samplesheet validation #112

merged 8 commits into from
Jul 24, 2023

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JoseEspinosa
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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

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.

@JoseEspinosa JoseEspinosa changed the base branch from master to dev July 21, 2023 10:47
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @JoseEspinosa,

It looks like this pull-request is has been made against the JoseEspinosa/nf-core-proteinfold master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the JoseEspinosa/nf-core-proteinfold dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

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github-actions bot commented Jul 21, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e888c1c

+| ✅ 148 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  10 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: lib/WorkflowProteinfold.groovy
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in check_samplesheet.py: Update the script to check the samplesheet
  • pipeline_todos - TODO string in check_samplesheet.py: Update the check_samplesheet function
  • pipeline_todos - TODO string in check_samplesheet.py: Update the column names for the input samplesheet
  • 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
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-21 11:46:22

nvnieuwk
nvnieuwk approved these changes Jul 24, 2023
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LGTM!

@JoseEspinosa JoseEspinosa merged commit 236d405 into nf-core:dev Jul 24, 2023
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@nvnieuwk nvnieuwk nvnieuwk approved these changes

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@JoseEspinosa @nvnieuwk