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Bwafallback #551

Merged
merged 25 commits into from
May 20, 2024
Merged

Bwafallback #551

merged 25 commits into from
May 20, 2024

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ramprasadn
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PR checklist

This PR adds an option to use bwamem as a fallback for bwamem2.

  • 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 May 17, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2d5c918

+| ✅ 183 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 2024-05-17 20:21:35

@ramprasadn ramprasadn marked this pull request as ready for review May 17, 2024 11:43
@ramprasadn ramprasadn requested review from rannick and jemten May 17, 2024 11:43
jemten
jemten reviewed May 17, 2024
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subworkflows/local/alignment/align_bwa_bwamem2.nf Outdated
Comment on lines 36 to 52

if (params.bwa_as_fallback.equals(true)) {
ch_reads_input
.join(BWAMEM2_MEM.out.bam, remainder: true)
.branch { it ->
ERROR: it[2].equals(null)
return [it[0], it[1]] // return reads
SUCCESS: !it[2].equals(null)
return [it[0], it[2]] // return bam
}
.set { ch_fallback }

BWAMEM_FALLBACK ( ch_fallback.ERROR, ch_bwa_index, true )
ch_align = ch_fallback.SUCCESS.mix(BWAMEM_FALLBACK.out.bam)
ch_versions = ch_versions.mix(BWAMEM_FALLBACK.out.versions.first())
}

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very clever 🌟

jemten
jemten approved these changes May 20, 2024
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Looks good

@ramprasadn ramprasadn merged commit 5e7b87e into dev May 20, 2024
6 checks passed
@ramprasadn ramprasadn deleted the bwafallback branch May 20, 2024 10:17
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@jemten jemten jemten approved these changes

@rannick rannick Awaiting requested review from rannick

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@ramprasadn @jemten @rannick