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Bump Deepvariant, add sample name arg #1992

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Merged
matthdsm merged 8 commits into from
Sep 23, 2025
Merged

Bump Deepvariant, add sample name arg #1992

matthdsm merged 8 commits into from
Sep 23, 2025

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@matthdsm
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@matthdsm matthdsm commented Sep 22, 2025 •
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  • Bump deepvariant to 1.9.0
  • Add --sample_name arg to deepvariant config

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/sarek branch on the nf-core/test-datasets repository.
  • 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.
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@matthdsm matthdsm requested a review from famosab September 22, 2025 13:09
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github-actions bot commented Sep 22, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4a9bd7b

+| ✅ 224 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗   7 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • 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!
  • schema_lint - Input mimetype is missing or empty
  • schema_description - No description provided in schema for parameter: markduplicates_pixel_distance
  • schema_description - No description provided in schema for parameter: gatk_pcr_indel_model

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-09-23 05:34:45

famosab
famosab reviewed Sep 22, 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",
meta.sample ? "--sample_name ${meta.sample}": "",
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does deepvariant version 1.8 support this already? otherwise we will need to update to 1.9 and update the snaps

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maxulysse commented Sep 22, 2025

I think we need

lint:
  schema_params: false

maxulysse
maxulysse reviewed Sep 22, 2025
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matthdsm and others added 2 commits September 22, 2025 15:28
@matthdsm matthdsm changed the title Add sample name arg to deepvariant Bump Deepvariant, add sample name arg Sep 22, 2025
famosab
famosab reviewed Sep 22, 2025
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famosab
famosab reviewed Sep 22, 2025
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famosab
famosab approved these changes Sep 22, 2025
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🚀 Lets see if the tests pass!

maxulysse
maxulysse approved these changes Sep 22, 2025
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just need to update snapshots, but it looks good to me

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matthdsm commented Sep 22, 2025

What's the password to update the snapshots?
nf-test test --verbose --profile test,docker --update-snapshot --clean-snapshot tests/variant_calling_deepvariant.nf.test ?

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famosab commented Sep 22, 2025

Honestly I just run
nf-test test --profile test,docker --update-snapshot tests/variant_calling_deepvariant.nf.test
usually that works :) so your command should do it

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matthdsm commented Sep 22, 2025 •
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Could someone else fix up the snapshots? the multiqc container doesn't agree with my mac...

EDIT: nvm, was able to fix it on another server

@matthdsm matthdsm enabled auto-merge September 23, 2025 05:32
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maxulysse commented Sep 23, 2025

Any idea why the VCF changed snapshots?
Is the header changing or the variants?

@matthdsm matthdsm merged commit a673ac9 into dev Sep 23, 2025
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matthdsm commented Sep 23, 2025

Sorry, I didn't check...

@famosab famosab deleted the config/deepvariant_sample_name branch September 30, 2025 09:43
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@maxulysse maxulysse maxulysse approved these changes

@famosab famosab famosab approved these changes

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

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@matthdsm @maxulysse @famosab