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 --skip_dada_addspecies #352

Merged
merged 2 commits into from Nov 16, 2021
Merged

Add --skip_dada_addspecies #352

merged 2 commits into from Nov 16, 2021

Conversation

d4straub
Copy link
Collaborator

@d4straub d4straub commented Nov 12, 2021 •
edited

DADA2's taxonomic classification on species level with addSpecies can be peak memory (RAM) requirement for the pipeline. Here the --skip_dada_addspecies is added to be able to skip that step when memory (RAM) is limiting.
However, --skip_dada_addspecies is incompatible with --cut_its and --sbdiexport because those expect species level annotation currently.

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).
  • 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 Nov 12, 2021 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 268a83c

+| ✅ 136 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.

✅ Tests passed:

Run details

  • nf-core/tools version 2.1
  • Run at 2021-11-12 15:05:17

erikrikarddaniel
erikrikarddaniel approved these changes Nov 16, 2021
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.

LGTM

@d4straub
Copy link
Collaborator Author

Thanks!

@d4straub d4straub merged commit e9afede into nf-core:dev Nov 16, 2021
@d4straub d4straub deleted the add-skip_dada_addspecies branch November 16, 2021 09:10
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.

None yet
2 participants
@d4straub @erikrikarddaniel