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 cnvkit genemetrics #1223

Merged
merged 18 commits into from
Oct 16, 2023
Merged

Add cnvkit genemetrics #1223

merged 18 commits into from
Oct 16, 2023

Conversation

grantn5
Copy link
Contributor

@grantn5 grantn5 commented Sep 12, 2023 •
edited
Loading

PR checklist

This PR adds the genemetrics module to CNVkit which creates an extra genemetrics file. Showing CNVs on a per gene level. If annotation is present, else an empty file is made

  • 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).

@grantn5 grantn5 requested a review from maxulysse as a code owner September 12, 2023 08:49
@github-actions
Copy link

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @grantn5,

It looks like this pull-request is has been made against the grantn5/sarek master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the grantn5/sarek dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@grantn5 grantn5 changed the base branch from master to dev September 12, 2023 08:51
@maxulysse
Copy link
Member

Hi @grantn5,
We're about to release soon, so we'll probably merge your PR after, and it'll be available for the next one, which will be fairly soon as well

@FriederikeHanssen
Copy link
Contributor

Hey! Thanks for adding this. Looks like you might not be quite up to date on the dev branch, the Changelog is missing quite some things. Can you merge in dev?

@grantn5
Copy link
Contributor Author

grantn5 commented Sep 12, 2023 •
edited
Loading

Hey! Thanks for adding this. Looks like you might not be quite up to date on the dev branch, the Changelog is missing quite some things. Can you merge in dev?

Hey, That should be done!

@github-actions
Copy link

github-actions bot commented Sep 19, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9ea1aad

+| ✅ 147 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-16 16:24:31

maxulysse
maxulysse reviewed Sep 20, 2023
View reviewed changes
CHANGELOG.md Outdated Show resolved Hide resolved
@FriederikeHanssen
Copy link
Contributor

Hey! Sorry for the delay once this PR is merged the tests should be triggered automatically. Did you test the genemetrics implementation on some data already? I am just wondering if the gene name display works properly, because we currently still have a feature request open to the refFlat file.

@FriederikeHanssen
Copy link
Contributor

@nf-core-bot fix linting

@grantn5
Copy link
Contributor Author

grantn5 commented Oct 12, 2023 •
edited
Loading

Hey! Sorry for the delay once this PR is merged the tests should be triggered automatically. Did you test the genemetrics implementation on some data already? I am just wondering if the gene name display works properly, because we currently still have a feature request open to the refFlat file.

Hi Yes I have tested that it works on some of my own data, i usually annotate my data with a bed file from ensembl and it the names appear fine.
Do you mean you have a feature request open on sarek or CNVkit?

@FriederikeHanssen
Copy link
Contributor

@nf-core-bot fix linting

@FriederikeHanssen
Copy link
Contributor

@maxulysse can you review, Grant and me pair-programmed the PR now :D

asp8200
asp8200 reviewed Oct 16, 2023
View reviewed changes
CHANGELOG.md Outdated Show resolved Hide resolved
asp8200
asp8200 reviewed Oct 16, 2023
View reviewed changes
CHANGELOG.md Outdated Show resolved Hide resolved
@maxulysse
Copy link
Member

@maxulysse can you review, Grant and me pair-programmed the PR now :D

Looking good, I think we're just missing the commented line in the output block

@FriederikeHanssen FriederikeHanssen merged commit c9bff2e into nf-core:dev Oct 16, 2023
22 checks passed
@grantn5 grantn5 deleted the add_cnvkit_genemetrics branch October 17, 2023 09:15
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@asp8200 asp8200 asp8200 left review comments

@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

@maxulysse maxulysse maxulysse left review comments

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
5 participants
@grantn5 @maxulysse @FriederikeHanssen @asp8200 @nf-core-bot