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

Run barrnap with fasta #535

Merged
merged 4 commits into from
Feb 8, 2023
Merged

Run barrnap with fasta #535

merged 4 commits into from
Feb 8, 2023

Conversation

erikrikarddaniel
Copy link
Member

@erikrikarddaniel erikrikarddaniel commented Feb 7, 2023 •
edited
Loading

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).

Barrnap is now called also with fasta input. In addition, although not tested, filtering should work with fasta input.

@github-actions
Copy link

github-actions bot commented Feb 7, 2023

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @erikrikarddaniel,

It looks like this pull-request is has been made against the erikrikarddaniel/ampliseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the erikrikarddaniel/ampliseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@erikrikarddaniel erikrikarddaniel changed the base branch from master to dev February 7, 2023 17:20
@github-actions
Copy link

github-actions bot commented Feb 7, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a6675ec

+| ✅ 155 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 2.7.2
  • Run at 2023-02-08 15:02:52

d4straub
d4straub approved these changes Feb 8, 2023
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.

Looks good to me, except that

ampliseq/docs/usage.md

Line 185 in 83877d2

When pointing at a file ending with `.fasta`, `.fna` or `.fa`, the containing ASV/OTU sequences will be taxonomically classified. All other pipeline steps will be skipped.
should state that ITSx & Barrnap & length filtering can be applied before taxonomic classification.

@erikrikarddaniel erikrikarddaniel merged commit cbe14ab into nf-core:dev Feb 8, 2023
@erikrikarddaniel erikrikarddaniel deleted the run-barrnap-with-fasta branch February 8, 2023 15:43
@d4straub d4straub mentioned this pull request Feb 9, 2023
Closed
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
@erikrikarddaniel @d4straub