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Change vep_version to vep_cache_version in ENSEMBLVEP_VEP-config #1294

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Change vep_version to vep_cache_version in ENSEMBLVEP_VEP-config #1294

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asp8200
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@asp8200 asp8200 commented Oct 23, 2023

Just changing params.vep_version to params.vep_cache_version in config of ENSEMBLVEP_VEP since params.vep_version is depricated.

TO-DO: Update changelog ;-)

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.
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@asp8200
Changing params.vep_version to params.vep_cache_version in config of …
9464d32 
…ENSEMBLVEP_VEP since params.vep_version is depricated.
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github-actions bot commented Oct 23, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9464d32

+| ✅ 144 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.
  • schema_description - No description provided in schema for parameter: bcftools_annotations
  • schema_description - No description provided in schema for parameter: bcftools_annotations_index
  • schema_description - No description provided in schema for parameter: bcftools_header_lines

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-23 14:28:09

@asp8200 asp8200 changed the title Chang vep_version to vep_cache_version in ENSEMBLVEP_VEP-config Change vep_version to vep_cache_version in ENSEMBLVEP_VEP-config Oct 23, 2023
@FriederikeHanssen
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Thanks. Can you also sync the nextflow_schema.json? There are also a couple of leftovers in the sarek.nf

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asp8200 commented Oct 26, 2023

Hi Rike. Maxime wrote to me "I'm afraid your proposed changes won't be working", but nevertheless wanted me to keep this PR open:

https://nfcore.slack.com/archives/C05V9FRJYMV/p1698137473172509?thread_ts=1698066953.775229&cid=C05V9FRJYMV

I'm sure he'll sort this out when he is back in action.

@maxulysse maxulysse mentioned this pull request Oct 31, 2023
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@maxulysse maxulysse closed this Oct 31, 2023
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@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen will be requested when the pull request is marked ready for review FriederikeHanssen is a code owner

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse will be requested when the pull request is marked ready for review maxulysse is a code owner

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@asp8200 @FriederikeHanssen @maxulysse