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

Dp24 module update samtools #333

Merged
merged 14 commits into from
Nov 21, 2024
Merged

Dp24 module update samtools #333

merged 14 commits into from
Nov 21, 2024

Conversation

DLBPointon
Copy link
Contributor

Updates to the SAMTOOLS modules

Means simplifying a small section in hic_bamtobed.

Other modules will be done in larger groups or we will be here all year.

@DLBPointon DLBPointon added documentation Improvements or additions to documentation enhancement New feature or request labels Nov 20, 2024
@DLBPointon DLBPointon added this to the Release 1 milestone Nov 20, 2024
@DLBPointon DLBPointon self-assigned this Nov 20, 2024
@github-actions GitHub Actions
Copy link

github-actions bot commented Nov 20, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 85217d9

+| ✅ 127 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '1.2.0'
  • pipeline_todos - TODO string in methods_description_template.yml: ## Update the HTML below to your prefered 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
  • system_exit - System.exit in WorkflowTreeval.groovy: System.exit(1) [line 17]

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_dark.png
  • files_exist - File is ignored: conf/igenomes.config
  • 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
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • 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/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_dark.png
  • 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/treeval/treeval/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2024-11-21 14:39:10

@DLBPointon
Copy link
Contributor Author

Key notes:

  • Pinning BUSCO to v5.5

    • Using 5.7 would cause a reproducible and very odd crash on Actions

  • Versions in CHANGELOG need updating.

@yumisims yumisims merged commit 7a0ca25 into dev Nov 21, 2024
6 checks passed
@DLBPointon DLBPointon deleted the dp24_module_update_samtools branch November 21, 2024 16:00
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@weaglesBio weaglesBio weaglesBio approved these changes

@yumisims yumisims Awaiting requested review from yumisims

Assignees

@DLBPointon DLBPointon

Labels
documentation Improvements or additions to documentation enhancement New feature or request
Projects
None yet
Milestone
Release 1
Development

Successfully merging this pull request may close these issues.
3 participants
@DLBPointon @weaglesBio @yumisims