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add bait regions to deepvariant for WES #633

Merged
merged 5 commits into from
Oct 16, 2024
Merged

add bait regions to deepvariant for WES #633

merged 5 commits into from
Oct 16, 2024

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ramprasadn
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PR checklist

Addresses #631

  • 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).

@ramprasadn ramprasadn mentioned this pull request Oct 14, 2024
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github-actions bot commented Oct 14, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7e0cad7

+| ✅ 200 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

❔ 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 3.0.2
  • Run at 2024-10-16 17:33:05

@ramprasadn ramprasadn marked this pull request as ready for review October 15, 2024 06:39
@fellen31
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From the outside, something that's a bit unclear to me is the difference between call_intervals and --target_bed + --bait_padding.

jemten
jemten approved these changes Oct 16, 2024
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👍

@ramprasadn
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--call_intervals is only used by sentieon. I have clarified that in the schema now @fellen31

@ramprasadn ramprasadn merged commit cdf7263 into dev Oct 16, 2024
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@ramprasadn ramprasadn deleted the deepvar-for-regions branch October 17, 2024 06:49
@jemten jemten mentioned this pull request Oct 22, 2024
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@ramprasadn @fellen31 @jemten