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add parameter --skip_variant_calling #169

Merged
merged 8 commits into from
Oct 15, 2024
Merged

add parameter --skip_variant_calling #169

merged 8 commits into from
Oct 15, 2024

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Lucpen
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@Lucpen Lucpen commented Oct 15, 2024

PR checklist

  • add parameter --skip_variant_calling to speed things up if you want to build a database with drop
  • 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 pipelines 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).

@Lucpen Lucpen requested a review from a team as a code owner October 15, 2024 09:44
@Lucpen Lucpen linked an issue Oct 15, 2024 that may be closed by this pull request
Add switch for variant calling #148
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github-actions bot commented Oct 15, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fc5f676

+| ✅ 180 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: 2.2.1
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-tomte_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-tomte_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-tomte_logo_dark.png
  • files_exist - File is ignored: docs/images/tomte_logo.eps
  • files_exist - File is ignored: docs/images/tomte_pipeline_metromap.svg
  • files_exist - File is ignored: docs/images/tomte_pipeline_metromap.png
  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • 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 does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-tomte_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-tomte_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-tomte_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/tomte/tomte/.github/workflows/awstest.yml
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-15 13:45:19

Lucpen
Lucpen commented Oct 15, 2024
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Lucpen
Lucpen commented Oct 15, 2024
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@Lucpen Lucpen added enhancement New feature or request Ready for review Ready for review labels Oct 15, 2024
fellen31
fellen31 approved these changes Oct 15, 2024
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@fellen31 fellen31 left a comment

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Just one question, otherwise LGTM! 👍

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@Lucpen Lucpen merged commit 3e2df59 into dev Oct 15, 2024
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@Lucpen Lucpen deleted the switch_variant_call branch October 15, 2024 14:07
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Add switch for variant calling
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@Lucpen @fellen31