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New tool: parabricks/indexgvcf #4141

Merged
merged 21 commits into from
Dec 13, 2023
Merged

New tool: parabricks/indexgvcf #4141

merged 21 commits into from
Dec 13, 2023

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Furentsu
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@Furentsu Furentsu commented Oct 18, 2023 •
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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 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

@Furentsu Furentsu requested a review from a team as a code owner October 18, 2023 09:41
auto-merge was automatically disabled December 12, 2023 16:36

Head branch was pushed to by a user without write access

maxulysse
maxulysse reviewed Dec 12, 2023
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almost perfect

@maxulysse maxulysse added this pull request to the merge queue Dec 13, 2023
Merged via the queue into nf-core:master with commit 8d916a6 Dec 13, 2023
10 checks passed
lrauschning pushed a commit to lrauschning/modules that referenced this pull request Dec 21, 2023
@Furentsu @mashehu
@maxulysse @bsiranosian @lrauschning
New tool: parabricks/indexgvcf (nf-core#4141)
ba39f63 
* new tool - indexgvcf

* removed trailing whitespace in modules/nf-core/parabricks/indexgvcf/main.nf

* run prettier on tests/modules/nf-core/parabricks/indexgvcf/test.yml

* modified config file for indexgvcf

* modified pbrun command params

* modified meta description of input file

* run prettier

* fixed main.nf

* changed config file

* Update modules/nf-core/parabricks/indexgvcf/main.nf

Co-authored-by: Matthias Hörtenhuber <[email protected]>

* fixed typo in config

* feat: get indexgvcf working. Update container, allow multiple file extensions in output, remove disallowed options

* feat: update tests to stage file with expected filename. factor out gpu options

* feat: update meta

* feat: exclude conda gha

* added bsiranosian as author

* Update modules/nf-core/parabricks/indexgvcf/meta.yml

Co-authored-by: Maxime U Garcia <[email protected]>

---------

Co-authored-by: Matthias Hörtenhuber <[email protected]>
Co-authored-by: Maxime U Garcia <[email protected]>
Co-authored-by: Ben Siranosian <[email protected]>
Co-authored-by: Maxime U Garcia <[email protected]>
lrauschning pushed a commit to lrauschning/modules that referenced this pull request Jan 17, 2024
@Furentsu @mashehu
@maxulysse @bsiranosian @lrauschning
New tool: parabricks/indexgvcf (nf-core#4141)
3fdfe35 
* new tool - indexgvcf

* removed trailing whitespace in modules/nf-core/parabricks/indexgvcf/main.nf

* run prettier on tests/modules/nf-core/parabricks/indexgvcf/test.yml

* modified config file for indexgvcf

* modified pbrun command params

* modified meta description of input file

* run prettier

* fixed main.nf

* changed config file

* Update modules/nf-core/parabricks/indexgvcf/main.nf

Co-authored-by: Matthias Hörtenhuber <[email protected]>

* fixed typo in config

* feat: get indexgvcf working. Update container, allow multiple file extensions in output, remove disallowed options

* feat: update tests to stage file with expected filename. factor out gpu options

* feat: update meta

* feat: exclude conda gha

* added bsiranosian as author

* Update modules/nf-core/parabricks/indexgvcf/meta.yml

Co-authored-by: Maxime U Garcia <[email protected]>

---------

Co-authored-by: Matthias Hörtenhuber <[email protected]>
Co-authored-by: Maxime U Garcia <[email protected]>
Co-authored-by: Ben Siranosian <[email protected]>
Co-authored-by: Maxime U Garcia <[email protected]>
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@maxulysse maxulysse maxulysse left review comments

@mashehu mashehu mashehu left review comments

@adamrtalbot adamrtalbot adamrtalbot approved these changes

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@Furentsu @maxulysse @mashehu @adamrtalbot @bsiranosian