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Add option to restrict analysis to specific contigs #644

Merged
merged 11 commits into from
Nov 11, 2024
Merged

Add option to restrict analysis to specific contigs #644

merged 11 commits into from
Nov 11, 2024

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ramprasadn
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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/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 Nov 8, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c98d063

+| ✅ 201 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 2024-11-11 21:02:42

@ramprasadn ramprasadn marked this pull request as ready for review November 9, 2024 09:13
@fellen31
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In long-reads I imagine this strategy would not call translocations with one good breakpoint in an interesting gene on 1-22, X, Y and the other breakpoint mapping to a few different places (including unplaced contigs).

Would this be an issue here?

@ramprasadn
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Hi Felix! We have added the option to restrict the analysis to chromosomes only because alignments to unplaced contigs can be messy, leading to less reliable results. We want to minimize any potential errors from those alignments.

fellen31
fellen31 reviewed Nov 11, 2024
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Could you add to the usage documentation?

Otherwise it looks good to me. I'd lean towards using a BED-file rather than a regions string, but both work.

@fellen31
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Hi Felix! We have added the option to restrict the analysis to chromosomes only because alignments to unplaced contigs can be messy, leading to less reliable results. We want to minimize any potential errors from those alignments.

Makes sense to not deal with such variants at all, thanks for clarifying!

fellen31
fellen31 approved these changes Nov 11, 2024
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👍

jemten
jemten approved these changes Nov 11, 2024
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subworkflows/local/alignment/align_bwa_bwamem2_bwameme.nf Outdated Show resolved Hide resolved
subworkflows/local/alignment/align_sentieon.nf Outdated Show resolved Hide resolved
@ramprasadn ramprasadn merged commit afea4ff into dev Nov 11, 2024
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@jemten jemten deleted the samtools_view branch November 12, 2024 08:13
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@fellen31 fellen31 fellen31 approved these changes

@jemten jemten jemten approved these changes

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@ramprasadn @fellen31 @jemten