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Bcftools sort new syntax #1169

Merged
merged 11 commits into from
Jan 5, 2022
Merged

Bcftools sort new syntax #1169

merged 11 commits into from
Jan 5, 2022

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Gwennid
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@Gwennid Gwennid commented Dec 14, 2021 •
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PR checklist

Closes #915

This PR adds the bcftools/sort utility, which can be useful subworkflows manipulating VCFs.

  • 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
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd

@Gwennid Gwennid added new module Adding a new module draft labels Dec 14, 2021
@Gwennid Gwennid self-assigned this Dec 14, 2021
@Gwennid Gwennid marked this pull request as ready for review December 20, 2021 16:18
grst
grst approved these changes Jan 4, 2022
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LGTM!

@Gwennid
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Gwennid commented Jan 5, 2022

LGTM!

Thanks!

@Gwennid Gwennid merged commit 2d4b0f7 into nf-core:master Jan 5, 2022
@Gwennid Gwennid deleted the bcftools-sort-new-syntax branch January 5, 2022 11:16
@Gwennid Gwennid mentioned this pull request Jan 5, 2022
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@grst grst grst approved these changes

@projectoriented projectoriented Awaiting requested review from projectoriented

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new module: bcftools/sort
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