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SVDB_MERGE bgzip#1910

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WackerO merged 6 commits intonf-core:masterfrom
WackerO:svdb
Jul 20, 2022
Merged

SVDB_MERGE bgzip#1910
WackerO merged 6 commits intonf-core:masterfrom
WackerO:svdb

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@WackerO WackerO commented Jul 20, 2022

This PR adds a bgzip command to the SVDB MERGE module to compress the output VCF.

  • 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

Comment thread tests/modules/svdb/merge/test.yml Outdated
@WackerO WackerO merged commit 8214b73 into nf-core:master Jul 20, 2022
@WackerO WackerO deleted the svdb branch July 20, 2022 08:54
@WackerO WackerO restored the svdb branch July 20, 2022 10:33
This was referenced Jul 20, 2022
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3 participants