Skip to content
New issue

Have a question about this project? # for a free GitHub account to open an issue and contact its maintainers and the community.

#

By clicking “#”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? # to your account

Jump to bottom

Code suggestions #140

Merged
merged 3 commits into from
Sep 15, 2023
Merged

Code suggestions #140

merged 3 commits into from
Sep 15, 2023

Conversation

muffato
Copy link
Member

@muffato muffato commented Sep 15, 2023

Here I'm proposing two changes:

  • The code for computing the duration works in a toy example - but I haven't tested it in TreeVal
  • I think github is not a great variable name. What about simply on using config_profile_name ?

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
  • 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).

@muffato muffato requested a review from DLBPointon September 15, 2023 14:52
@muffato muffato mentioned this pull request Sep 15, 2023
Merged
@github-actions
Copy link

github-actions bot commented Sep 15, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e9dd94d

+| ✅ 125 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: '1.0.0'
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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
  • 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
  • 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 2023-09-15 15:43:26

@DLBPointon
Update TreeValProject.groovy
e9dd94d 
Adding the Duration import and .toSeconds()
DLBPointon
DLBPointon requested changes Sep 15, 2023
View reviewed changes
Copy link
Contributor

@DLBPointon DLBPointon left a comment

Choose a reason for hiding this comment

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

It works!

Just a couple of changes. Thanks for the help @muffato

@DLBPointon DLBPointon merged commit 87d2635 into pre-tag Sep 15, 2023
@DLBPointon DLBPointon deleted the mm49_pre_tag branch September 15, 2023 15:56
# for free to join this conversation on GitHub. Already have an account? # to comment
Reviewers

@DLBPointon DLBPointon DLBPointon requested 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
@muffato @DLBPointon