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allow vep 112 #617

Merged
merged 4 commits into from
Sep 26, 2024
Merged

allow vep 112 #617

merged 4 commits into from
Sep 26, 2024

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jemten
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@jemten jemten commented Sep 24, 2024 •
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PR checklist

The vep module uses version 112, yet the pipeline does not allow the cache to be set to that version

  • 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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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 Sep 24, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e583e15

+| ✅ 187 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-25 20:10:14

ramprasadn
ramprasadn reviewed Sep 24, 2024
View reviewed changes
nextflow_schema.json Outdated
"description": "Specify the version of the VEP cache provided to the `--vep_cache` option.",
"fa_icon": "fas fa-align-center",
"enum": [107, 110]
"enum": [107, 110, 112]
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Should we allow 111 as well?

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Kind of thinking we should remove this enum altogether and just have the requirement on it being a number.

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Yeah, that's better actually 😅

@ramprasadn ramprasadn merged commit 985230b into dev Sep 26, 2024
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@ramprasadn ramprasadn deleted the add_vep_112_option branch October 1, 2024 14:19
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@ramprasadn ramprasadn ramprasadn approved these changes

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@jemten @ramprasadn