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Use original QC values for Deepvariant after BQSR #1733

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Use original QC values for Deepvariant after BQSR #1733

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@FriederikeHanssen
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Closes #682

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!
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maxulysse
maxulysse previously approved these changes Nov 15, 2024
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github-actions bot commented Nov 16, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7ae5034

+| ✅ 215 tests passed       |+
#| ❔  11 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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 base.config: Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-19 09:08:42

@FriederikeHanssen
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Can't get the described flags to work. Asked about here: google/deepvariant#908

@FriederikeHanssen
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Tests are currently failing because the test data does not have bqsr quality scores. We need to swap out the data used for deepvariant testing

@FriederikeHanssen FriederikeHanssen marked this pull request as draft November 19, 2024 09:07
@FriederikeHanssen FriederikeHanssen mentioned this pull request Aug 21, 2025
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famosab
famosab reviewed Aug 21, 2025
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conf/modules/deepvariant.config
ext.args = { params.wes ? "--model_type=WES" : "--model_type=WGS" }
ext.args = [
params.wes ? "--model_type=WES" : "--model_type=WGS" ,
!params.skip_tools?.contains("baserecalibrator") ? "--make_examples_extra_args '--parse_sam_aux_fields=true,--use_original_quality_scores=true'" : ''
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Suggested change
!params.skip_tools?.contains("baserecalibrator") ? "--make_examples_extra_args '--parse_sam_aux_fields=true,--use_original_quality_scores=true'" : ''
!params.skip_tools?.contains("baserecalibrator") ? "--make_examples_extra_args 'parse_sam_aux_fields=true,use_original_quality_scores=true'" : ''

That way it works for me.

@famosab famosab linked an issue Aug 21, 2025 that may be closed by this pull request
Deepvariant requires additional cli option for recalibrated BAM files #682
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Deepvariant requires additional cli option for recalibrated BAM files

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@FriederikeHanssen @maxulysse @famosab