Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Merged
merged 8 commits into from
Jul 12, 2023
Merged

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

merged 8 commits into from
Jul 12, 2023

Conversation

drpatelh
Copy link
Member

@drpatelh drpatelh commented Jul 6, 2023 •
edited
Loading

  • 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
Closed
@github-actions
Copy link

github-actions bot commented Jul 6, 2023 •
edited
Loading

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
View reviewed changes
Copy link

@nvnieuwk nvnieuwk left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This looks very good!

workflows/rnaseq.nf Outdated Show resolved Hide resolved
@drpatelh
Copy link
Member Author

@nf-core-bot fix linting

nvnieuwk
nvnieuwk approved these changes Jul 12, 2023
View reviewed changes
Copy link

@nvnieuwk nvnieuwk left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM

@mirpedrol mirpedrol mentioned this pull request Jul 12, 2023
Merged
10 tasks
@drpatelh drpatelh merged commit c6bfe7a into nf-core:dev Jul 12, 2023
26 checks passed
@mirpedrol mirpedrol mentioned this pull request Aug 10, 2023
Closed
@drpatelh drpatelh deleted the updates branch October 11, 2023 20:43
@pinin4fjords pinin4fjords mentioned this pull request Nov 8, 2023
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@nvnieuwk nvnieuwk nvnieuwk approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
3 participants
@drpatelh @nvnieuwk @nf-core-bot