Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fix AMRFinderPlus database #365

Merged
merged 5 commits into from
Apr 25, 2024
Merged

Fix AMRFinderPlus database #365

merged 5 commits into from
Apr 25, 2024

Conversation

jasmezz
Copy link
Collaborator

@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
@github-actions GitHub Actions
Copy link

github-actions bot commented Apr 24, 2024 •
edited
Loading

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
View reviewed changes
Copy link
Contributor

@Darcy220606 Darcy220606 left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks fine to me 👍🏽

docs/usage.md Outdated Show resolved Hide resolved
jasmezz
jasmezz commented Apr 25, 2024
View reviewed changes
docs/usage.md Outdated Show resolved Hide resolved
@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
Closed
@jasmezz jasmezz mentioned this pull request Jul 29, 2024
Merged
10 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@Darcy220606 Darcy220606 Darcy220606 approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@jasmezz @Darcy220606