Skip to content

Cleanup #73

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
Merged
matthdsm merged 11 commits into from
Oct 12, 2023
Merged

Cleanup #73

matthdsm merged 11 commits into from
Oct 12, 2023

Conversation

@matthdsm
Copy link
Member

@matthdsm matthdsm commented Oct 11, 2023

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
    • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
    • If necessary, also make a PR on the CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@github-actions
Copy link

github-actions bot commented Oct 11, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fa613b9

+| ✅ 121 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗  13 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: lib/WorkflowNf-cmgg-preprocessing.groovy
  • readme - README did not have a Nextflow minimum version badge.
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in full.config: Give any required params for the test so that command line flags are not needed
  • 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
  • pipeline_todos - TODO string in WorkflowCmggpreprocessing.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_name_conventions - Naming does not adhere to nf-core conventions: Contains non alphanumeric characters
  • schema_lint - Parameter input not found in schema

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-nf-cmgg-preprocessing_logo_light.png
  • files_exist - File is ignored: conf/test.config
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: docs/images/nf-core-nf-cmgg-preprocessing_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nf-cmgg-preprocessing_logo_dark.png
  • files_exist - File is ignored: lib/nfcore_external_java_deps.jar
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • nextflow_config - Config variable ignored: params.input
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-nf-cmgg-preprocessing_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nf-cmgg-preprocessing_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nf-cmgg-preprocessing_logo_dark.png
  • files_unchanged - File does not exist: lib/nfcore_external_java_deps.jar
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/nf-cmgg-preprocessing/nf-cmgg-preprocessing/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-12 07:00:23

@matthdsm matthdsm merged commit f9d31c4 into dev Oct 12, 2023
@matthdsm matthdsm deleted the cleanup branch October 12, 2023 08:31
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

2 participants

@matthdsm