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GATK CNVCaller fixes #472

Merged
merged 12 commits into from
Jan 10, 2024
Merged

GATK CNVCaller fixes #472

merged 12 commits into from
Jan 10, 2024

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Jakob37
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@Jakob37 Jakob37 commented Jan 10, 2024 •
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This PR attempts to fix three issues (#442, #444, #450) that was necessary to change to be able to run GATK CNVCaller.

  1. Use segments instead of intervals (the intervals are the initial bins with are linked together into longer segments to make the final "calls").
  2. Filter the "reference" segments from the GATK output. I didn't find any built-in way to directly remove these from the output, so I filtered it using BCFTOOLS.
  3. Update the processing of the ch_readcount_intervals variable (it contains just a path, but was handled as a tuple with meta + path).

It is testrun locally with no errors. It ends up as expected in the SVDB merged output.

Comments are warmly welcome. Guidance on how to approach wrapping this from here is appreciated.

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).
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@Jakob37 Jakob37 changed the title Jw/gatk fixes GATK CNVCaller fixes Jan 10, 2024
This was linked to issues Jan 10, 2024
params.readcount_intervals are not handled correctly for use in CNV-caller #442
Closed
Use segments output instead of intervals from CNV-caller #444
Closed
Filter reference segments from CNV caller output #450
Closed
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github-actions bot commented Jan 10, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 938591d

+| ✅ 155 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowRaredisease.groovy: Optionally add in-text citation tools to this list.

❔ 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
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-10 09:05:53

@jemten
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jemten commented Jan 10, 2024

ready for review @Jakob37?

@Jakob37 Jakob37 marked this pull request as ready for review January 10, 2024 12:46
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Jakob37 commented Jan 10, 2024

@jemten Yes!

ramprasadn
ramprasadn approved these changes Jan 10, 2024
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LGTM!

@jemten jemten merged commit 4f50a3e into nf-core:dev Jan 10, 2024
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@ramprasadn ramprasadn ramprasadn approved these changes

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