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.

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

Clarify clip_readlength help text for what is considered ultra-short … #891

Merged
merged 2 commits into from
Jul 4, 2022

Conversation

jfy133
Copy link
Member

@jfy133 jfy133 commented May 30, 2022

…reads

Closes #887

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).

@github-actions
Copy link

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!

@github-actions
Copy link

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!

@jfy133 jfy133 linked an issue May 30, 2022 that may be closed by this pull request
Copy link
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 d2dd49f into dev Jul 4, 2022
@jfy133 jfy133 deleted the patch-improve_clipreadlength_desc branch July 4, 2022 11:52
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.

Clarify "very short reads" in helptext of clip_readlength
3 participants