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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

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grantn5
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@grantn5 grantn5 commented Sep 12, 2023 •
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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).

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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
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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
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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
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grantn5 commented Sep 12, 2023 •
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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!

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github-actions bot commented Sep 19, 2023 •
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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
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@FriederikeHanssen
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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
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@nf-core-bot fix linting

@grantn5
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grantn5 commented Oct 12, 2023 •
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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
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@nf-core-bot fix linting

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

asp8200
asp8200 reviewed Oct 16, 2023
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asp8200
asp8200 reviewed Oct 16, 2023
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@maxulysse
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@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
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@grantn5 grantn5 deleted the add_cnvkit_genemetrics branch October 17, 2023 09:15
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@grantn5 @maxulysse @FriederikeHanssen @asp8200 @nf-core-bot