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 lib folder #132

Merged
merged 20 commits into from
Mar 1, 2024
Merged

Remove lib folder #132

merged 20 commits into from
Mar 1, 2024

Conversation

JoseEspinosa
Copy link
Member

Remove lib/ directory and replace with nf-core subworkflows.

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.

@github-actions GitHub Actions
Copy link

github-actions bot commented Feb 29, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 663fa13

+| ✅ 182 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗  11 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • 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 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
  • 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 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

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.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 2.13.1
  • Run at 2024-03-01 09:50:10

luisas
luisas approved these changes Mar 1, 2024
View reviewed changes
CHANGELOG.md Outdated
@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [[#113](https://github.com/nf-core/proteinfold/pull/113)] - Include esmfold dbs for full data sets.
- [[PR #114](https://github.com/nf-core/rnaseq/pull/114)] - Update paths to test dbs.
- [[PR #117](https://github.com/nf-core/proteinfold/pull/117)] - Update pipeline template to [nf-core/tools 2.10](https://github.com/nf-core/tools/releases/tag/2.10).
- [PR #130](https://github.com/nf-core/proteinfold/pull/130) - Remove `lib/` directory.
Copy link
Contributor

Choose a reason for hiding this comment

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

Suggested change
- [PR #130](https://github.com/nf-core/proteinfold/pull/130) - Remove `lib/` directory.
- [[PR #130](https://github.com/nf-core/proteinfold/pull/130)] - Remove `lib/` directory.

Copy link
Member Author

Choose a reason for hiding this comment

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

Good spot and actually is #132 😓

main.nf
PREPARE_ALPHAFOLD2_DBS.out.uniprot
)
ch_multiqc = ALPHAFOLD2.out.multiqc_report
ch_versions = ch_versions.mix(ALPHAFOLD2.out.versions)
}

//
// WORKFLOW: Run colabfold
//
else if(params.mode == "colabfold") {
Copy link
Contributor

Choose a reason for hiding this comment

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

If we just leave it if instead of else if, we can have the option Cedric wanted, of running multiple tools in the same run.
What do you think?

Copy link
Contributor

Choose a reason for hiding this comment

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

We would have to mix the channels of versions and multiqc too, i am not sure how tricky it would be for multiqc

Copy link
Member Author

Choose a reason for hiding this comment

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

This will be for a different PR, will open an issue though. Also, I am starting to think that we could do it for a 1.2 version and leave this one as it is.

@JoseEspinosa JoseEspinosa merged commit 835e2fd into nf-core:dev Mar 1, 2024
7 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@luisas luisas luisas 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.
2 participants
@JoseEspinosa @luisas