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Fix AMRFinderPlus database #365

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Merged
merged 5 commits into from
Apr 25, 2024
Merged

Fix AMRFinderPlus database #365

merged 5 commits into from
Apr 25, 2024

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jasmezz
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@jasmezz jasmezz commented Apr 24, 2024

  • Updates the amrfinderplus/run module into the pipeline
  • Update the usage docs as to how to supply a local database (removed the NCBI download part because that alone did not work. The user would have to index/create blast database files, which seems more complicated (skimming through the code from AMRFinderPlus amrfinder_index.cpp file). So just using the update command from conda seems more reasonable.

This also solves #328

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/funcscan 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,singularity --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).

@jasmezz jasmezz requested a review from a team April 24, 2024 14:06
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github-actions bot commented Apr 24, 2024 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 1f709f9

+| ✅ 236 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-24 14:13:56

Darcy220606
Darcy220606 approved these changes Apr 25, 2024
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Looks fine to me 👍🏽

jasmezz
jasmezz commented Apr 25, 2024
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@jasmezz jasmezz merged commit 7947522 into dev Apr 25, 2024
@jasmezz jasmezz deleted the fix-amrfinderplus branch April 25, 2024 09:31
@jasmezz jasmezz mentioned this pull request Apr 25, 2024
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@jasmezz jasmezz mentioned this pull request Jul 29, 2024
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@Darcy220606 Darcy220606 Darcy220606 approved these changes

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@jasmezz @Darcy220606
点击 这是indexloc提供的php浏览器服务，不要输入任何密码和下载