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Replace grep with ripgrep for expensive searches #43

Merged
merged 2 commits into from
May 28, 2024
Merged

Replace grep with ripgrep for expensive searches #43

merged 2 commits into from
May 28, 2024

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itrujnara
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5-10x speedup for no effort. I consider this a win.
There was a manual merge in fetch_oma_group_local.nf so please double-check nothing broke.

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).

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github-actions bot commented May 28, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8de588c

+| ✅ 217 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗  10 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-28 10:16:11

luisas
luisas approved these changes May 28, 2024
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I have approved it but add ripgerp also on eggnog :)

modules/local/fetch_eggnog_group_local.nf
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it still uses grep here

@itrujnara itrujnara merged commit 2da7da1 into nf-core:dev May 28, 2024
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@luisas luisas luisas approved these changes

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@itrujnara @luisas