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feat: add VEP module#547

Merged
maxulysse merged 13 commits intonf-core:masterfrom
maxulysse:master_vep
Jul 6, 2021
Merged

feat: add VEP module#547
maxulysse merged 13 commits intonf-core:masterfrom
maxulysse:master_vep

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PR checklist

Closes #215

  • 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 <SOFTWARE>.version.txt 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

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@grst grst left a comment

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A few questions/comments, otherwise LGTM!

Comment thread software/ensemblvep/main.nf
Comment thread tests/software/ensemblvep/main.nf
Comment thread software/ensemblvep/meta.yml
@drpatelh drpatelh added the new module Adding a new module label Jul 5, 2021
Comment thread software/ensemblvep/build.sh
Comment thread software/ensemblvep/environment.yml Outdated
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Comment thread software/ensemblvep/environment.yml
Comment thread software/ensemblvep/main.nf Outdated
Comment thread software/ensemblvep/main.nf Outdated
Comment thread software/ensemblvep/main.nf Outdated
Comment thread software/ensemblvep/main.nf Outdated
Comment thread software/ensemblvep/main.nf
@drpatelh drpatelh mentioned this pull request Jul 6, 2021
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Comment thread software/ensemblvep/main.nf Outdated
Comment thread software/ensemblvep/main.nf Outdated
Comment thread software/ensemblvep/main.nf Outdated
Comment thread software/ensemblvep/meta.yml Outdated
Comment thread software/ensemblvep/meta.yml Outdated
Comment thread software/ensemblvep/meta.yml Outdated
Comment thread software/ensemblvep/meta.yml Outdated
Comment thread software/ensemblvep/meta.yml Outdated
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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@drpatelh drpatelh left a comment

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Amazing! Thanks @maxulysse!

@maxulysse maxulysse merged commit 7b4a28b into nf-core:master Jul 6, 2021
@maxulysse maxulysse deleted the master_vep branch July 6, 2021 12:11
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new module: ensembl-vep

3 participants