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

Synchronize example samplesheets with the usage.md #362

Merged
merged 2 commits into from
Jun 25, 2024
Merged

Synchronize example samplesheets with the usage.md #362

merged 2 commits into from
Jun 25, 2024

Conversation

bjlang
Copy link
Contributor

@bjlang bjlang commented Apr 12, 2024

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 nf-core/atacseq 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 GitHub Actions
Copy link

github-actions bot commented Apr 12, 2024 •
edited
Loading

nf-core lint overall result: Failed ❌

Posted for pipeline commit e69f5dc

+| ✅ 215 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   6 tests had warnings |!
-| ❌   4 tests failed       |-

❌ Test failures:

  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • base_config - conf/base.config contains withName:CUSTOM_DUMPSOFTWAREVERSIONS, but the corresponding process is not present in any of the Nextflow scripts.

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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
  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.bamtools_filter_pe_config
  • nextflow_config - Config default ignored: params.bamtools_filter_se_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-10 13:14:01

JoseEspinosa
JoseEspinosa approved these changes Jun 25, 2024
View reviewed changes
Copy link
Member

@JoseEspinosa JoseEspinosa left a comment

Choose a reason for hiding this comment

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

LGTM

@JoseEspinosa JoseEspinosa merged commit 510563e into nf-core:dev Jun 25, 2024
10 of 11 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@JoseEspinosa JoseEspinosa JoseEspinosa 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
2 participants
@bjlang @JoseEspinosa