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

Remove phytoref #710

Merged
merged 6 commits into from
Mar 18, 2024
Merged

Remove phytoref #710

merged 6 commits into from
Mar 18, 2024

Conversation

danilodileo
Copy link
Contributor

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/ampliseq 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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

Phytoref is included in PR2 5.0.0 so I removed it from DADA references option.

@github-actions GitHub Actions
Copy link

github-actions bot commented Mar 18, 2024 •
edited
Loading

nf-core lint overall result: Failed ❌

Posted for pipeline commit daa9dce

+| ✅ 180 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!
-| ❌  10 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/WorkflowAmpliseq.groovy
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/branch.yml 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
  • files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-18 09:28:33

@d4straub
Copy link
Collaborator

Hi,
there is a recent problem with nf-core template & most recent nextflow version. I'll resolve that after #702 is done. So failing tests are expected!

Also remove the entry from nextflow_schema.json please.

@danilodileo
Copy link
Contributor Author

Hi, there is a recent problem with nf-core template & most recent nextflow version. I'll resolve that after #702 is done. So failing tests are expected!

Also remove the entry from nextflow_schema.json please.

Hi Daniel,
so can we just merge even if the errors are there?

d4straub
d4straub approved these changes Mar 18, 2024
View reviewed changes
Copy link
Collaborator

@d4straub d4straub left a comment

Choose a reason for hiding this comment

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

LGTM

CHANGELOG.md Outdated
@@ -17,6 +17,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#677](https://github.com/nf-core/ampliseq/pull/677) - Added cut_its information to SDBI export

- [#710](https://github.com/nf-core/ampliseq/pull/710) - Removed Phyloref from DADA2 reference option because it's part of PR2 5.0.0
Copy link
Collaborator

Choose a reason for hiding this comment

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

May be best under "removed" fine as well here.

@d4straub
Copy link
Collaborator

so can we just merge even if the errors are there?

Yes, I can merge that. Just let me know and I'll do it.

@danilodileo
Copy link
Contributor Author

so can we just merge even if the errors are there?

Yes, I can merge that. Just let me know and I'll do it.

It's ready to be merged!

@d4straub d4straub merged commit e366469 into nf-core:dev Mar 18, 2024
2 of 16 checks passed
@d4straub d4straub mentioned this pull request Mar 18, 2024
Closed
@danilodileo danilodileo deleted the remove-phytoref branch January 20, 2025 11:18
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@d4straub d4straub d4straub approved these changes

@erikrikarddaniel erikrikarddaniel Awaiting requested review from erikrikarddaniel

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
@danilodileo @d4straub