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 ability to skip fastq/falco #325

Merged
merged 3 commits into from
Jul 15, 2023
Merged

Add ability to skip fastq/falco #325

merged 3 commits into from
Jul 15, 2023

Conversation

jfy133
Copy link
Member

@jfy133 jfy133 commented Jul 14, 2023 •
edited
Loading

closes #324

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/taxprofiler 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).

@jfy133 jfy133 requested a review from a team July 14, 2023 06:28
@github-actions
Copy link

github-actions bot commented Jul 14, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4e38c36

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-14 11:24:03

@jfy133
Copy link
Member Author

jfy133 commented Jul 14, 2023

Passes locally even if tests fail due to the upstream taxpasta bug(just waiting for the biocontainer)

mirpedrol
mirpedrol approved these changes Jul 14, 2023
View reviewed changes
Copy link
Member

@mirpedrol mirpedrol left a comment

Choose a reason for hiding this comment

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

LGTM

@jfy133
Copy link
Member Author

jfy133 commented Jul 14, 2023

Thanks @mirpedrol ! I just merged in the fix for the CI test, so I'll marge that back in here and hopefully all the tests pass :)

Midnighter
Midnighter approved these changes Jul 14, 2023
View reviewed changes
Copy link
Collaborator

@Midnighter Midnighter 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 😃

@jfy133 jfy133 merged commit 71c9275 into dev Jul 15, 2023
20 checks passed
@jfy133 jfy133 deleted the skip-fastq-falco branch July 15, 2023 05:28
@jfy133 jfy133 linked an issue Jul 17, 2023 that may be closed by this pull request
Add functionality to turn read QC on/off #324
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@Midnighter Midnighter Midnighter approved these changes

@mirpedrol mirpedrol mirpedrol 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.

Add functionality to turn read QC on/off
3 participants
@jfy133 @Midnighter @mirpedrol