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Update selectvariants #4896

Merged
merged 5 commits into from
Feb 12, 2024
Merged

Update selectvariants #4896

merged 5 commits into from
Feb 12, 2024

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ramprasadn
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PR checklist

this PR removes ".selectvariants" suffix added to vcf files by default and switches pytest out for nf-test

  • 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

@ramprasadn ramprasadn marked this pull request as ready for review February 12, 2024 16:02
@ramprasadn ramprasadn requested review from mjcipriano and a team as code owners February 12, 2024 16:02
@ramprasadn ramprasadn requested review from Aratz, jemten and Lucpen and removed request for a team February 12, 2024 16:02
Lucpen
Lucpen approved these changes Feb 12, 2024
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@Lucpen Lucpen left a comment

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LGTM!

@ramprasadn ramprasadn added this pull request to the merge queue Feb 12, 2024
Merged via the queue into nf-core:master with commit 47cd015 Feb 12, 2024
11 checks passed
@ramprasadn ramprasadn deleted the selectvariants branch February 12, 2024 16:18
jch-13 pushed a commit to jch-13/modules that referenced this pull request Mar 19, 2024
@ramprasadn @jch-13
Update selectvariants (nf-core#4896)
e0c8adf 
* update tests

* remove slectvariants suffix

* update tags

* fix typo

* update tests
jennylsmith pushed a commit to RSC-RP/modules that referenced this pull request Mar 20, 2024
@ramprasadn @jennylsmith
Update selectvariants (nf-core#4896)
91b3c9d 
* update tests

* remove slectvariants suffix

* update tags

* fix typo

* update tests
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@Lucpen Lucpen Lucpen approved these changes

@mjcipriano mjcipriano Awaiting requested review from mjcipriano

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

@jemten jemten Awaiting requested review from jemten

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2 participants
@ramprasadn @Lucpen