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Add sentieon/dnascope from nf-core/modules#406

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ramprasadn merged 7 commits into
nf-core:devfrom
genomic-medicine-sweden:dnascope
Aug 18, 2023
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Add sentieon/dnascope from nf-core/modules#406
ramprasadn merged 7 commits into
nf-core:devfrom
genomic-medicine-sweden:dnascope

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@ramprasadn

@ramprasadn ramprasadn commented Aug 17, 2023

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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>).
  • 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 Aug 17, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2f47cd1

+| ✅ 151 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ 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: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-17 16:01:46

@ramprasadn ramprasadn marked this pull request as ready for review August 17, 2023 18:49
@ramprasadn ramprasadn requested a review from asp8200 August 18, 2023 08:34
asp8200
asp8200 reviewed Aug 18, 2023
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Comment thread workflows/raredisease.nf
: Channel.empty()
ch_ml_model = params.variant_caller.equals("sentieon") ? Channel.fromPath(params.ml_model).collect()
: Channel.value([])
ch_ml_model = params.variant_caller.equals("sentieon") ? Channel.fromPath(params.ml_model).map {it -> [[id:it[0].simpleName], it]}.collect()

@asp8200 asp8200 Aug 18, 2023

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Just curious, when using params.variant_caller.equals("sentieon") it kind of indicates that the raredisease-pipeline is designed to only use one variant-caller per run of the pipeline - is that correct?

@ramprasadn ramprasadn Aug 18, 2023

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Yes, that is correct 😄

asp8200
asp8200 approved these changes Aug 18, 2023
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LGTM

@ramprasadn ramprasadn merged commit e58c7ef into nf-core:dev Aug 18, 2023
@ramprasadn ramprasadn deleted the dnascope branch August 22, 2023 10:37
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@ramprasadn @asp8200