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Allow CAT_DB to take a directory containing the CAT database #372

Merged
merged 7 commits into from
Jan 31, 2023
Merged

Allow CAT_DB to take a directory containing the CAT database #372

merged 7 commits into from
Jan 31, 2023

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prototaxites
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@prototaxites prototaxites commented Dec 20, 2022 •
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One last little one from me before the holidays. Allow CAT_DB to take a directory containing the CAT database, rather than just a tar.gz file - when working with a local copy of the database, saves approximately an hour on the tar.gz extraction.

Also fixes an issue with the cat_official_taxonomy parameter I added before, where I had a brain fart writing the code and included the wrong flag in the CAT add_names command.

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

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github-actions bot commented Dec 20, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a338fb7

+| ✅ 156 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-01-16 09:19:12

@prototaxites
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@nf-core-bot fix linting

@prototaxites prototaxites requested a review from d4straub January 26, 2023 13:16
d4straub
d4straub approved these changes Jan 31, 2023
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LGTM, but I didnt actually test it, did you?

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It was before Christmas, but I did test it and it works happily both with a zip or a directory - CAT ran happily either way. Can re-run if you think it's needed?

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I think thats fine, feel free to merge it ;)

@prototaxites prototaxites merged commit 4b215b7 into nf-core:dev Jan 31, 2023
@prototaxites prototaxites deleted the fast_cat_db branch January 31, 2023 09:31
@jfy133 jfy133 mentioned this pull request Feb 27, 2023
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@d4straub d4straub d4straub approved these changes

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