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

bugfix: param_list needs to be initialised #165

Merged
merged 3 commits into from
Feb 8, 2025
Merged

bugfix: param_list needs to be initialised #165

merged 3 commits into from
Feb 8, 2025

Conversation

muffato
Copy link
Member

@muffato muffato commented Feb 7, 2025

Closes TOLIT-2834

Sort-of tested with

fetch_ensembl_metadata.py --taxon_id 1870436 --output GCA_934047225.1_ensembl_annotation.csv

though the problem only strikes when the API call to the Ensembl GraphQL API fails.

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 added the bug Something isn't working label Feb 7, 2025
@muffato muffato requested a review from gq1 February 7, 2025 17:25
@muffato muffato self-assigned this Feb 7, 2025
@github-actions GitHub Actions
Copy link

github-actions bot commented Feb 8, 2025 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d096d7c

+| ✅ 131 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-genomenote_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomenote_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomenote_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/igenomes.config
  • 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 does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File does not exist: assets/nf-core-genomenote_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomenote_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomenote_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/genomenote/genomenote/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2025-02-08 12:28:54

gq1
gq1 approved these changes Feb 8, 2025
View reviewed changes
Copy link
Member

@gq1 gq1 left a comment

Choose a reason for hiding this comment

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

upload-artifact v3 causing failure now, not like I tested last time.

Here fixed now.

@muffato
Copy link
Member Author

muffato commented Feb 8, 2025

upload-artifact v3 causing failure now, not like I tested last time.

I wonder of it's because you did your tests before the deadline of Jan 31st. So things were still working at the time, but now that we're in Feb, they've really removed v3

@muffato muffato merged commit a00f9f7 into dev Feb 8, 2025
6 checks passed
@muffato muffato deleted the variable_initialisation branch February 8, 2025 15:48
@gq1
Copy link
Member

gq1 commented Feb 8, 2025

upload-artifact v3 causing failure now, not like I tested last time.
but now that we're in Feb, they've really removed v3
This is good and then force people to fix.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@gq1 gq1 gq1 approved these changes

Assignees

@muffato muffato

Labels
bug Something isn't working
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@muffato @gq1