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Add subsample mt #508

Merged
merged 18 commits into from
Feb 2, 2024
Merged

Add subsample mt #508

merged 18 commits into from
Feb 2, 2024

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ramprasadn
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PR checklist

Addresses #497

  • 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).

@ramprasadn ramprasadn marked this pull request as ready for review February 2, 2024 10:05
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github-actions bot commented Feb 2, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cf6c313

+| ✅ 182 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowRaredisease.groovy: Optionally add in-text citation tools to this list.
  • 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: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-02 15:00:24

@ramprasadn ramprasadn requested review from Lucpen and jemten and removed request for Lucpen February 2, 2024 10:10
jemten
jemten approved these changes Feb 2, 2024
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Small comments but looks good otherwise

docs/output.md Outdated
@@ -115,6 +116,18 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
- `*.metrics`: Text file containing the dedup metrics.
</details>

#### Subsample mitochondrial alignments

[Samtools view](https://www.htslib.org/doc/samtools-view.html) is used by the pipeline to subsample mitochondrial alignments to a user specified coverage.
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Suggested change
[Samtools view](https://www.htslib.org/doc/samtools-view.html) is used by the pipeline to subsample mitochondrial alignments to a user specified coverage.
[Samtools view](https://www.htslib.org/doc/samtools-view.html) is used by the pipeline to subsample mitochondrial alignments to a user specified coverage. The file is mainly intended to be used for visualization of MT alignments in IGV. The non-subsampled bam file is used for variant calling and other downstream analysis steps.

subworkflows/local/subsample_mt.nf Outdated
Comment on lines 28 to 34
)
.csv
.join(ch_mt_bam_bai, failOnMismatch:true)
.map{meta, seedfrac, bam, bai ->
return [meta + [seedfrac: file(seedfrac).text.readLines()[0]], bam, bai]
}
.set { ch_subsample_in }
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Could you fix the indentation of this part. Think it needs to be left shifted by one level

@ramprasadn ramprasadn merged commit 561bdcc into nf-core:dev Feb 2, 2024
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@ramprasadn ramprasadn deleted the subsample_mt branch February 2, 2024 16:56
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@jemten jemten jemten approved these changes

@Lucpen Lucpen Awaiting requested review from Lucpen

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@ramprasadn @jemten