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odgi sort/layout power up #86

Merged
merged 1 commit into from
Sep 16, 2022
Merged

odgi sort/layout power up #86

merged 1 commit into from
Sep 16, 2022

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subwaystation
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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
    • If necessary, also make a PR on the nf-core/pangenome 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).

Update to the latest PGGB docker image which accelerates the 1D PG-SGD algorithm up to ~8 fold pangenome/odgi#445 and the 2D PG-SGD algorithm up to ~7 fold pangenome/odgi#446.

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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!

@subwaystation subwaystation merged commit 34149c6 into dev Sep 16, 2022
@heuermh heuermh deleted the odgi_sort_layout_power_up branch February 22, 2024 16:13
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