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Allow ONT with HiFiCNV #233

Merged
merged 7 commits into from
Jul 1, 2024
Merged

Allow ONT with HiFiCNV #233

merged 7 commits into from
Jul 1, 2024

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fellen31
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@fellen31 fellen31 commented Jun 28, 2024 •
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This PR allows the CNV-calling workflow to be run with ONT data.

Should be merged after #231.

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
  • 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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github-actions bot commented Jun 28, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f3b044c

+| ✅ 157 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗  13 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your 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!
  • 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 test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • schema_description - No description provided in schema for parameter: hificnv_xy
  • schema_description - No description provided in schema for parameter: hificnv_xx

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-nallo_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nallo_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nallo_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-nallo_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-28 14:11:30

@fellen31 fellen31 added the Ready for review This PR is ready for review label Jul 1, 2024
@fellen31 fellen31 marked this pull request as ready for review July 1, 2024 08:41
@fellen31 fellen31 requested a review from a team as a code owner July 1, 2024 08:41
jemten
jemten approved these changes Jul 1, 2024
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Looks good!

@fellen31 fellen31 merged commit d9873c6 into genomic-medicine-sweden:dev Jul 1, 2024
8 checks passed
@fellen31 fellen31 deleted the allow-ont-hificnv branch July 1, 2024 08:57
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@jemten jemten jemten approved these changes

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