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Add cnvnator subworkflow #434

Merged
merged 11 commits into from
Nov 13, 2023
Merged

Add cnvnator subworkflow #434

merged 11 commits into from
Nov 13, 2023

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ramprasadn
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@ramprasadn ramprasadn commented Oct 16, 2023 •
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PR checklist

Closes #433

  • 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).

@ramprasadn ramprasadn requested a review from jemten October 16, 2023 16:31
@ramprasadn ramprasadn marked this pull request as ready for review October 16, 2023 16:31
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github-actions bot commented Oct 16, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b80ed16

+| ✅ 151 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 2.10
  • Run at 2023-11-13 17:15:22

jemten
jemten reviewed Oct 27, 2023
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@jemten jemten left a comment

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Nice work! One thing that should be checked before merging is the sample names in the vcf file. If I remember correctly conver2vcf will use the path of the starting bam minus the .bam ending as sample name. This would need to be changed to the original sample name. The vcf also lacks contigs in the header, which could be an issue downstream. Could you check this and also confirm that it is compatible with the downstream steps, ie merging the different caller sets?

@ramprasadn
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Tested with a full dataset, and it works!

@ramprasadn ramprasadn merged commit 5dae2b9 into nf-core:dev Nov 13, 2023
8 checks passed
@jemten jemten deleted the cnvnator branch November 14, 2023 07:58
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@ramprasadn @jemten