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

Unhide params trim_fastq, umi_read_structure, and aligner. #1179

Merged
merged 4 commits into from
Aug 15, 2023
Merged

Unhide params trim_fastq, umi_read_structure, and aligner. #1179

merged 4 commits into from
Aug 15, 2023

Conversation

robsyme
Copy link
Contributor

@robsyme robsyme commented Aug 14, 2023

Minor PR to unhide three parameters that are arguably used often enough to make the list of those made visible-by-default.

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/sarek 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).

@robsyme
Unhide params trim_fastq, umi_read_structure, and aligner.
7ab8c61 
Signed-off-by: Rob Syme <rob.syme@gmail.com>
@robsyme
Copy link
Contributor Author

robsyme commented Aug 14, 2023

Addressing issue #1170

@github-actions
Copy link

github-actions bot commented Aug 14, 2023 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6a840e7

+| ✅ 151 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-15 11:00:18

FriederikeHanssen
FriederikeHanssen approved these changes Aug 14, 2023
View reviewed changes
Copy link
Contributor

@FriederikeHanssen FriederikeHanssen left a comment

Choose a reason for hiding this comment

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

great, thanks :) Can you add it to the Changelog? Approving, because it is later here already

asp8200
asp8200 reviewed Aug 14, 2023
View reviewed changes
nextflow_schema.json Outdated Show resolved Hide resolved
asp8200
asp8200 approved these changes Aug 14, 2023
View reviewed changes
Copy link
Contributor

@asp8200 asp8200 left a comment

Choose a reason for hiding this comment

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

Thanks, Rob

@robsyme @asp8200
Update nextflow_schema.json
b0d1248 
While here, remove backticks from Sarek and DragMap software names.

Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com>
maxulysse
maxulysse reviewed Aug 15, 2023
View reviewed changes
nextflow_schema.json Outdated Show resolved Hide resolved
maxulysse
maxulysse reviewed Aug 15, 2023
View reviewed changes
nextflow_schema.json Outdated Show resolved Hide resolved
robsyme and others added 2 commits August 15, 2023 06:57
@robsyme @maxulysse
Update nextflow_schema.json
cbe8ccd 
Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
@robsyme @maxulysse
Update nextflow_schema.json
6a840e7 
Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
@robsyme robsyme merged commit f9fd774 into nf-core:dev Aug 15, 2023
19 checks passed
@maxulysse
Copy link
Member

What about the CHANGELOG?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@maxulysse maxulysse maxulysse left review comments

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@asp8200 asp8200 asp8200 approved these changes

Assignees
No one assigned
Labels
None yet
Projects
Sarek Board
Status: Done
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
4 participants
@robsyme @maxulysse @FriederikeHanssen @asp8200