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move gatk4/mergevcfs to nf-test #4913

Merged
merged 6 commits into from
Feb 15, 2024
Merged

move gatk4/mergevcfs to nf-test #4913

merged 6 commits into from
Feb 15, 2024

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matthdsm
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PR checklist

Closes #XXX

  • 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:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

@matthdsm matthdsm requested review from KevinMenden and a team as code owners February 14, 2024 14:01
@matthdsm matthdsm requested review from leoisl and removed request for a team February 14, 2024 14:01
nvnieuwk
nvnieuwk reviewed Feb 14, 2024
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modules/nf-core/gatk4/mergevcfs/tests/main.nf.test
then {
assertAll(
{ assert process.success },
)
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Can you also check that the outputs get created in a stub run?

@matthdsm
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Can I get an approval here?

@maxulysse maxulysse added this pull request to the merge queue Feb 15, 2024
@matthdsm
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Thanks @maxulysse !

Merged via the queue into master with commit e71a1b0 Feb 15, 2024
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@maxulysse maxulysse deleted the nf-test/gatk4-mergevcfs branch February 15, 2024 07:48
jch-13 pushed a commit to jch-13/modules that referenced this pull request Mar 19, 2024
@matthdsm @nvnieuwk @jch-13
move gatk4/mergevcfs to nf-test (nf-core#4913)
75214fa 
* move gatk4/mergevcfs to nf-test

* Update modules/nf-core/gatk4/mergevcfs/tests/main.nf.test

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

* Update modules/nf-core/gatk4/mergevcfs/tests/main.nf.test

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

* fix tests

* Delete modules/nf-core/gatk4/mergevcfs/tests/nextflow.config

---------

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>
jennylsmith pushed a commit to RSC-RP/modules that referenced this pull request Mar 20, 2024
@matthdsm @nvnieuwk @jennylsmith
move gatk4/mergevcfs to nf-test (nf-core#4913)
79d2703 
* move gatk4/mergevcfs to nf-test

* Update modules/nf-core/gatk4/mergevcfs/tests/main.nf.test

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

* Update modules/nf-core/gatk4/mergevcfs/tests/main.nf.test

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>

* fix tests

* Delete modules/nf-core/gatk4/mergevcfs/tests/nextflow.config

---------

Co-authored-by: Nicolas Vannieuwkerke <[email protected]>
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@nvnieuwk nvnieuwk nvnieuwk left review comments

@maxulysse maxulysse maxulysse approved these changes

@KevinMenden KevinMenden Awaiting requested review from KevinMenden

@leoisl leoisl Awaiting requested review from leoisl leoisl was automatically assigned from nf-core/nf-test

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3 participants
@matthdsm @maxulysse @nvnieuwk