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Add found_in tag to vcf #471

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Merged
merged 6 commits into from
Jan 11, 2024
Merged

Add found_in tag to vcf #471

merged 6 commits into from
Jan 11, 2024

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ramprasadn
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PR checklist

#466

  • 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 Jan 10, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a64bd13

+| ✅ 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 2024-01-11 12:40:06

@ramprasadn ramprasadn marked this pull request as ready for review January 10, 2024 07:39
jemten
jemten reviewed Jan 10, 2024
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Nice work. Fun to see some groovy functions in action 😄

conf/test_one_sample.config
known_dbsnp = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz"
ml_model = "https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.0.model"
reduced_penetrance = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv"
score_config_mt = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini"
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👍

subworkflows/local/variant_calling/call_snv_sentieon.nf Outdated
TABIX_SEN(REMOVE_DUPLICATES_SEN.out.vcf)

ch_genome_fai.map{meta, fai ->
return [meta, WorkflowRaredisease.makeBedWithVariantCallerInfo(fai, fai.parent.toString(), "sentieon")]
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Could one do this operation fai.parent.toString() on the fai file in the function instead. Would reduce the clutter in the subworkflow.

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Another thing. I don't know the sentieon toolbox enough but maybe we should call this sentieon_dnascope to differentiate it from potential other sentieon algorithms.

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Sounds good! I will give it a try 👍🏻

@jemten jemten linked an issue Jan 10, 2024 that may be closed by this pull request
Tag each SNVs with the variant caller that was used #466
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jemten
jemten approved these changes Jan 11, 2024
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Looks good!

@ramprasadn ramprasadn merged commit 1b3c094 into nf-core:dev Jan 11, 2024
@ramprasadn ramprasadn deleted the found_by branch February 2, 2024 16:56
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Tag each SNVs with the variant caller that was used

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@ramprasadn @jemten
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