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 phylogenetic placement #564

Merged
merged 6 commits into from
Mar 29, 2023
Merged

Add phylogenetic placement #564

merged 6 commits into from
Mar 29, 2023

Conversation

d4straub
Copy link
Collaborator

@d4straub d4straub commented Mar 28, 2023 •
edited
Loading

Addresses #561

Missing:

  • there is a warning about a ".first()" in the added subworkflow. That is supposed to be solved when nf-core subworkflows patch is released
  • resulting files are not yet used by any downstream tool, this will need to be solved in a follow-up PR

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).

erikrikarddaniel
erikrikarddaniel approved these changes Mar 28, 2023
View reviewed changes
Copy link
Member

@erikrikarddaniel erikrikarddaniel left a comment

Choose a reason for hiding this comment

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

Great!

docs/output.md Outdated Show resolved Hide resolved
nextflow.config Outdated Show resolved Hide resolved
workflows/ampliseq.nf Outdated Show resolved Hide resolved
@github-actions
Copy link

github-actions bot commented Mar 28, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5aad68b

+| ✅ 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 2023-03-28 15:03:18

@d4straub d4straub merged commit d8fb16d into nf-core:dev Mar 29, 2023
@d4straub d4straub deleted the add-phylo-placement branch March 29, 2023 07:09
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@erikrikarddaniel erikrikarddaniel erikrikarddaniel 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
@d4straub @erikrikarddaniel