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Merged
merged 8 commits into from
Jan 12, 2024
Merged

Add bwa mem #474

merged 8 commits into from
Jan 12, 2024

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@ramprasadn
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@ramprasadn ramprasadn commented Jan 11, 2024 •
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PR checklist

Addresses #464

  • 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 11, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cbd9a24

+| ✅ 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 2024-01-12 10:15:14

@ramprasadn ramprasadn marked this pull request as ready for review January 11, 2024 08:11
@jemten jemten linked an issue Jan 11, 2024 that may be closed by this pull request
Add option to align with original bwa mem #464
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jemten
jemten approved these changes Jan 12, 2024
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Looks good! Just added a bwa to the help text for the aligner option

nextflow_schema.json
"aligner": {
"type": "string",
"default": "bwamem2",
"description": "Specifies the alignment algorithm to use - available options are 'bwamem2' and 'sentieon'.",
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Suggested change
"description": "Specifies the alignment algorithm to use - available options are 'bwamem2' and 'sentieon'.",
"description": "Specifies the alignment algorithm to use - available options are 'bwamem2', 'bwa' and 'sentieon'.",

@ramprasadn ramprasadn merged commit 7dea02a into nf-core:dev Jan 12, 2024
@jemten jemten deleted the bwamem branch January 22, 2024 11:02
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Add option to align with original bwa mem

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@ramprasadn @jemten