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

Added --save_intermediates #700

Merged
merged 3 commits into from
Feb 6, 2024
Merged

Added --save_intermediates #700

merged 3 commits into from
Feb 6, 2024

Conversation

d4straub
Copy link
Collaborator

@d4straub d4straub commented Feb 5, 2024 •
edited
Loading

Solves #694

With --save_intermediates many .qza and .qzv files of QIIME2 will be saved in the results folder. This parameter could be also more general in future.

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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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 Feb 5, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 739ccbd

+| ✅ 191 tests passed       |+
#| ❔   6 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 2.12.1
  • Run at 2024-02-06 09:15:38

jannikseidelQBiC
jannikseidelQBiC approved these changes Feb 6, 2024
View reviewed changes
Copy link

@jannikseidelQBiC jannikseidelQBiC left a comment

Choose a reason for hiding this comment

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

Left one comment, otherwise: LGTM!

nextflow.config Outdated Show resolved Hide resolved
@d4straub
Copy link
Collaborator Author

d4straub commented Feb 6, 2024 •
edited
Loading

Well, there is obviously a new nextflow version in use, namely 24.1.0-edge, which fails with
ERROR ~ Unknown method invocation `make_complement` on _parse_closure5 type
meaning its incompatible with a custom function of the pipeline... considering the linting succeeded before this version I go ahead and merge it. The problem requires a different PR it seems.

@d4straub d4straub merged commit 2a23b1b into nf-core:dev Feb 6, 2024
3 of 16 checks passed
@d4straub d4straub deleted the export-more-qza branch February 6, 2024 09:22
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jannikseidelQBiC jannikseidelQBiC jannikseidelQBiC 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 @jannikseidelQBiC