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Add a new paramter to skip sv calling #572

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Merged
merged 6 commits into from
Jun 24, 2024
Merged

Add a new paramter to skip sv calling #572

merged 6 commits into from
Jun 24, 2024

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@ramprasadn
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@ramprasadn ramprasadn commented Jun 24, 2024

Adds a new parameter skip_sv_calling

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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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).

@ramprasadn ramprasadn marked this pull request as ready for review June 24, 2024 12:37
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github-actions bot commented Jun 24, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 31e8f2e

+| ✅ 185 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-24 12:57:07

@ramprasadn ramprasadn requested review from Lucpen, jemten and rannick June 24, 2024 13:09
jemten
jemten approved these changes Jun 24, 2024
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Looks good

@ramprasadn ramprasadn merged commit 010da06 into dev Jun 24, 2024
@ramprasadn ramprasadn deleted the modularize-everything-2 branch June 24, 2024 13:25
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@jemten jemten jemten approved these changes

@rannick rannick Awaiting requested review from rannick

@Lucpen Lucpen Awaiting requested review from Lucpen

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@ramprasadn @jemten