Skip to content

Remove deprecated params from benchmarking profiles#892

Merged
jfy133 merged 4 commits intodevfrom
patch-testconfig_params_updates
Jul 4, 2022
Merged

Remove deprecated params from benchmarking profiles#892
jfy133 merged 4 commits intodevfrom
patch-testconfig_params_updates

Conversation

@jfy133
Copy link
Copy Markdown
Member

@jfy133 jfy133 commented May 30, 2022

Closes #889

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
    • If necessary, also make a PR on the nf-core/eager 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).
  • 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).

@jfy133 jfy133 requested a review from TCLamnidis May 30, 2022 18:18
@github-actions
Copy link
Copy Markdown

Markdown linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install markdownlint-cli
  • Fix the markdown errors
    • Automatically: markdownlint . --config .github/markdownlint.yml --fix
    • Manually resolve anything left from markdownlint . --config .github/markdownlint.yml

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

@jfy133 jfy133 linked an issue May 30, 2022 that may be closed by this pull request
@github-actions
Copy link
Copy Markdown

YAML linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install yaml-lint
  • Fix the markdown errors
    • Run the test locally: yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")
    • Fix any reported errors in your YAML files

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

Copy link
Copy Markdown
Collaborator

@TCLamnidis TCLamnidis left a comment

Choose a reason for hiding this comment

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

LGTM

@jfy133 jfy133 merged commit 8d41bc9 into dev Jul 4, 2022
@jfy133 jfy133 deleted the patch-testconfig_params_updates branch July 4, 2022 11:53
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

Update test configs

3 participants