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 phyloseq input #676

Merged
merged 4 commits into from
Dec 12, 2023
Merged

Fix phyloseq input #676

merged 4 commits into from
Dec 12, 2023

Conversation

d4straub
Copy link
Collaborator

@d4straub d4straub commented Dec 12, 2023 •
edited
Loading

Phyloseq produced qiime2_phyloseq.rds or pplace_phyloseq.rds for -profile test_pplace (but not both, even if it should!) and for -profile test_reftaxcustom it produced only one of dada2_phyloseq.rds or kraken2_phyloseq.rds. The problem seemed to be that the input asv table was a single entry of a channel that allowed only one of several taxonomic classification to be processed. I combined the channels so that this should be more flexible now.

Reproducible by e.g. repeatedly running nextflow run nf-core/ampliseq -r 2.7.1 -profile test_pplace,singularity --outdir result_test_pplace_2-7-1

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 GitHub Actions
Copy link

github-actions bot commented Dec 12, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 99b1db6

+| ✅ 154 tests passed       |+
#| ❔   3 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 2.10
  • Run at 2023-12-12 11:51:50

erikrikarddaniel
erikrikarddaniel approved these changes Dec 12, 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.

👍

@d4straub d4straub mentioned this pull request Dec 12, 2023
Merged
4 tasks
@d4straub d4straub mentioned this pull request Dec 12, 2023
Merged
6 tasks
@d4straub
Copy link
Collaborator Author

Thanks!

@d4straub d4straub merged commit 746c524 into nf-core:dev Dec 12, 2023
17 checks passed
@d4straub d4straub deleted the fix_phyloseq_input branch December 12, 2023 12:48
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