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Update dnascope-module #422

Merged
merged 4 commits into from
Sep 7, 2023
Merged

Update dnascope-module #422

merged 4 commits into from
Sep 7, 2023

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asp8200
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@asp8200 asp8200 commented Sep 5, 2023 •
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Updating sentieon-dnascope module.

Replacing params.pcr_amplification with params.sentieon_dnascope_pcr_indel_model.

Tested locally with

nextflow run main.nf -profile test_sentieon,docker --variant_caller sentieon

TO-DO: Update changelog.

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 Sep 5, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e867829

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

❗ 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 2023-09-07 10:03:45

@asp8200 asp8200 marked this pull request as ready for review September 5, 2023 18:01
ramprasadn
ramprasadn approved these changes Sep 7, 2023
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Two minor comments, but otherwise looks good! 👍🏻

@asp8200 asp8200 merged commit 44c218a into dev Sep 7, 2023
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@asp8200 asp8200 deleted the update_dnascope branch September 7, 2023 15:32
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@ramprasadn ramprasadn ramprasadn approved these changes

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