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non-working code, Julia to review python script and integration #178

Merged
merged 25 commits into from
Jul 23, 2024
Merged

non-working code, Julia to review python script and integration #178

merged 25 commits into from
Jul 23, 2024

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alan-tracey
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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/crisprseq 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).

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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 @alan-tracey,

It looks like this pull-request is has been made against the alan-tracey/crisprseq 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 alan-tracey/crisprseq 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!

@mirpedrol mirpedrol changed the base branch from master to dev July 22, 2024 10:24
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github-actions bot commented Jul 22, 2024 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 438c368

+| ✅ 223 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 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
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

  • files_exist - File is ignored: conf/test.config
  • files_exist - File is ignored: conf/test_full.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-23 15:08:00

mirpedrol
mirpedrol reviewed Jul 22, 2024
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Hi @alan-tracey, thanks for contributing with this feature!
I left some comments and code suggestions to show how to use a template, let me know if something is not clear enough :)

modules/local/clonality_classifier.nf Outdated Show resolved Hide resolved
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alan-tracey and others added 8 commits July 22, 2024 11:48
mirpedrol
mirpedrol reviewed Jul 23, 2024
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I have pushed the changes adding a parameter to allow skipping the new step (37c75c1) and published the file to the output directory (40063e0)

Leaving some last review comments, if all tests pass LGTM :)
We should add the change to CHANGELOG.md but we are in the middle of a patch release fixing a bug, and this PR deserves a minor version update, so it will be better to wait until we have done the patch release and then merge the PR.

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@mirpedrol
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@nf-core-bot fix linting please!

@mirpedrol
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Made some last fixes as the module was not running. These are the files generated from the test data.
chr6_edits_classified.csv
hCas9-AAVS1-a_edits_classified.csv
hCas9-TRAC-a_edits_classified.csv

@mirpedrol mirpedrol marked this pull request as ready for review July 23, 2024 15:03
@mirpedrol mirpedrol merged commit 8b5dfa5 into nf-core:dev Jul 23, 2024
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@LaurenceKuhl LaurenceKuhl mentioned this pull request Sep 17, 2024
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@mirpedrol mirpedrol mirpedrol approved these changes

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@alan-tracey @mirpedrol @nf-core-bot