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bwamem2 for mt #600

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Merged
merged 5 commits into from
Aug 20, 2024
Merged

bwamem2 for mt #600

merged 5 commits into from
Aug 20, 2024

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@ramprasadn
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@ramprasadn ramprasadn commented Aug 19, 2024

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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,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 19, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit af33552

+| ✅ 187 tests passed       |+
#| ❔   7 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/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • 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
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-20 08:22:25

@ramprasadn ramprasadn marked this pull request as ready for review August 19, 2024 15:00
@ramprasadn ramprasadn requested a review from jemten August 19, 2024 15:00
jemten
jemten reviewed Aug 20, 2024
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Looks good, a couple of comments
Need to update the mt_align config as well to remove these entries

raredisease/conf/modules/align_MT.config

Line 26 in b712e0c

withName: '.*ALIGN_MT:BWAMEME_MEM_MT' {

raredisease/conf/modules/align_MT.config

Line 83 in b712e0c

withName: '.*ALIGN_MT_SHIFT:BWAMEME_MEM_MT' {

CHANGELOG.md

### `Added`

- A new parameter `mt_aligner` to control which aligner is used to align reads to mitochondria [#600](https://github.com/nf-core/raredisease/pull/600)
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@jemten jemten Aug 20, 2024

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Could you add that bwa meme can no longer be used to align mt

@ramprasadn ramprasadn requested a review from jemten August 20, 2024 08:19
jemten
jemten approved these changes Aug 20, 2024
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LGTM

@ramprasadn ramprasadn merged commit 243c4b1 into dev Aug 20, 2024
@ramprasadn ramprasadn deleted the mito-update branch August 20, 2024 08:52
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@ramprasadn @jemten