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Save DRAMP in common database dir #275

Merged
merged 2 commits into from
May 12, 2023
Merged

Save DRAMP in common database dir #275

merged 2 commits into from
May 12, 2023

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jasmezz
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@jasmezz jasmezz commented May 12, 2023

Closes #271

Save DRAMP database in common database directory instead of in root directory when --save_databases flag is provided.

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,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).

@jasmezz jasmezz requested a review from a team May 12, 2023 12:19
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github-actions bot commented May 12, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1af35bd

+| ✅ 159 tests passed       |+
!| ❗   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 passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-05-12 12:20:45

louperelo
louperelo approved these changes May 12, 2023
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Looks good to me.
Could you add AMPcombi to the description of the --save_databases parameter in the nextflow_schema.json, so that it reads: "This applies to: BAKTA, DeepBGC, DeepARG, AMRFinderPlus, antiSMASH and AMPcombi"

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jasmezz commented May 12, 2023

Will do with [skip ci] after checks succeed.

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jasmezz commented May 12, 2023

Though I would call it DRAMP since it is not maintained by AMPcombi, but fetched from online.

@jasmezz jasmezz merged commit d0a1633 into dev May 12, 2023
@jasmezz jasmezz deleted the dramp-directory branch May 12, 2023 14:57
@jasmezz jasmezz mentioned this pull request May 17, 2023
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@louperelo louperelo louperelo approved these changes

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@jasmezz @louperelo