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

Add '_' to SH taxonomies to match UNITE database #491

Merged
merged 4 commits into from
Sep 22, 2022
Merged

Add '_' to SH taxonomies to match UNITE database #491

merged 4 commits into from
Sep 22, 2022

Conversation

jtangrot
Copy link
Contributor

This PR replaces spaces in SH taxonomies (from --addSH) with underscore, in order to match the format in the UNITE databases and by that the output from assignTaxonomy. E.g. "Eukaryota kgd Incertae sedis" is written as "Eukaryota_kgd_Incertae_sedis"

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/ampliseq 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).

@github-actions
Copy link

github-actions bot commented Sep 21, 2022 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0e96e8a

+| ✅ 151 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.5.1
  • Run at 2022-09-22 06:48:41

@d4straub
Copy link
Collaborator

Looks good to me, but black linting fails with would reformat bin/add_sh_to_taxonomy.py.
I'd recommend installing black and apply it.

@jtangrot
Copy link
Contributor Author

Looks good to me, but black linting fails with would reformat bin/add_sh_to_taxonomy.py. I'd recommend installing black and apply it.

Thanks for the suggestion! Fixed!

d4straub
d4straub approved these changes Sep 22, 2022
View reviewed changes
Copy link
Collaborator

@d4straub d4straub left a comment

Choose a reason for hiding this comment

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

LGTM!

@jtangrot jtangrot merged commit e5b845f into nf-core:dev Sep 22, 2022
@jtangrot
Copy link
Contributor Author

Thanks!

@jtangrot jtangrot deleted the sh_tax branch September 22, 2022 10:52
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@d4straub d4straub d4straub 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
@jtangrot @d4straub