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add new parameter to supply a bed like file for filtering vep results #511

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Merged
merged 7 commits into from
Feb 7, 2024
Merged

add new parameter to supply a bed like file for filtering vep results #511

merged 7 commits into from
Feb 7, 2024

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@ramprasadn
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@ramprasadn ramprasadn commented Feb 4, 2024

PR checklist

Addresses #498

  • 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>).
  • 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 Feb 4, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f6d4d6b

+| ✅ 182 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowRaredisease.groovy: Optionally add in-text citation tools to this list.
  • 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/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-07 08:39:44

@ramprasadn ramprasadn marked this pull request as ready for review February 4, 2024 19:58
ramprasadn
ramprasadn commented Feb 5, 2024
View reviewed changes
.github/workflows/ci.yml
Comment on lines 32 to +39
steps:
- name: Free some space
run: |
sudo rm -rf /usr/share/dotnet
sudo rm -rf /opt/ghc
sudo rm -rf "/usr/local/share/boost"
sudo rm -rf "$AGENT_TOOLSDIRECTORY"
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@ramprasadn ramprasadn Feb 5, 2024

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This bit clears up certain tools that come along with the github runner thereby leaving more space for the containers used in the pipeline.

rannick
rannick approved these changes Feb 7, 2024
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Nice work!

ramprasadn and others added 2 commits February 7, 2024 09:37
@ramprasadn @rannick
Update CHANGELOG.md
41221fd 
Co-authored-by: Annick Renevey <[email protected]>
@ramprasadn @rannick
Update nextflow_schema.json
f6d4d6b 
Co-authored-by: Annick Renevey <[email protected]>
@ramprasadn ramprasadn merged commit e8ac075 into nf-core:dev Feb 7, 2024
@ramprasadn ramprasadn deleted the filtervep-options branch February 7, 2024 08:49
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@rannick rannick rannick approved these changes

@jemten jemten Awaiting requested review from jemten

@Lucpen Lucpen Awaiting requested review from Lucpen

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@ramprasadn @rannick