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Move all vep args from ext.args to params.vep_custom_args #1157

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maxulysse merged 2 commits into from
Jul 20, 2023
Merged

Move all vep args from ext.args to params.vep_custom_args #1157

maxulysse merged 2 commits into from
Jul 20, 2023

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@maxulysse maxulysse commented Jul 20, 2023

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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jul 20, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 76120fd

+| ✅ 152 tests passed       |+
#| ❔   9 tests were ignored |#
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❔ Tests ignored:

✅ Tests passed:

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  • nf-core/tools version 2.9
  • Run at 2023-07-20 09:55:01

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asp8200 commented Jul 20, 2023

That should work fine. Can you just remind me why you want to move the vep args from ext.args to params.vep_custom_args?

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maxulysse commented Jul 20, 2023

That should work fine. Can you just remind me why you want to move the vep args from ext.args to params.vep_custom_args?

Because it's a mess to actually update any args in the ext.args.
So by moving all default args in the params, it'll be easier for users to just add or remove a single one.
Also I'm guessing we can actually work on the vcf output for VEP since it was vcf by default and without any way to change

@maxulysse maxulysse merged commit 967c248 into nf-core:dev Jul 20, 2023
@maxulysse maxulysse deleted the vep_custom_args branch July 20, 2023 10:28
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@maxulysse @asp8200