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Merged
LouisLeNezet merged 12 commits into from
Dec 11, 2025
Merged

Update GLIMPSE sbwf #9524

LouisLeNezet merged 12 commits into from
Dec 11, 2025

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@LouisLeNezet LouisLeNezet commented Dec 8, 2025 •
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PR checklist

Update GLIMPSE imputation subworkflow.

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@LouisLeNezet LouisLeNezet self-assigned this Dec 8, 2025
@LouisLeNezet LouisLeNezet marked this pull request as ready for review December 8, 2025 18:49
nvnieuwk
nvnieuwk reviewed Dec 11, 2025
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nvnieuwk
nvnieuwk reviewed Dec 11, 2025
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nvnieuwk
nvnieuwk reviewed Dec 11, 2025
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nvnieuwk
nvnieuwk reviewed Dec 11, 2025
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nvnieuwk
nvnieuwk approved these changes Dec 11, 2025
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A couple small comments for clarification, otherwise it LGTM

LouisLeNezet and others added 6 commits December 11, 2025 11:39
@LouisLeNezet @nvnieuwk
Update subworkflows/nf-core/vcf_impute_glimpse/main.nf
de3a85a 
Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
@LouisLeNezet @nvnieuwk
Update subworkflows/nf-core/vcf_impute_glimpse/main.nf
df9d7e9 
Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
@LouisLeNezet @nvnieuwk
Update subworkflows/nf-core/vcf_impute_glimpse/main.nf
d147254 
Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
@LouisLeNezet @nvnieuwk
Update subworkflows/nf-core/vcf_impute_glimpse/main.nf
2c9bb2e 
Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
@LouisLeNezet
Update snapshot
87e1ce0
@LouisLeNezet
Merge branch 'master' into sbwf_glimpse
abc3d82
@LouisLeNezet LouisLeNezet added this pull request to the merge queue Dec 11, 2025
Merged via the queue into nf-core:master with commit a2ae628 Dec 11, 2025
38 checks passed
@LouisLeNezet LouisLeNezet deleted the sbwf_glimpse branch December 11, 2025 11:01
vagkaratzas pushed a commit that referenced this pull request Dec 12, 2025
@LouisLeNezet @nvnieuwk @vagkaratzas
Update GLIMPSE sbwf (#9524)
37dbe45 
* Update glimpse sbwf

* Update test

* Update filter operation

* Update subworkflows/nf-core/vcf_impute_glimpse/main.nf

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

* Update subworkflows/nf-core/vcf_impute_glimpse/main.nf

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

* Update subworkflows/nf-core/vcf_impute_glimpse/main.nf

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

* Update subworkflows/nf-core/vcf_impute_glimpse/main.nf

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

* Update snapshot

---------

Co-authored-by: LouisLeNezet <louislenezet@gmaio.com>
Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
@LouisLeNezet LouisLeNezet mentioned this pull request Dec 13, 2025
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