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fixes #65 (renamed subworkflow, add missing bai ch) #75

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merged 3 commits into from
Dec 3, 2024
Merged

fixes #65 (renamed subworkflow, add missing bai ch) #75

merged 3 commits into from
Dec 3, 2024

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iraiosub
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@iraiosub iraiosub commented Dec 2, 2024 •
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Fixes #65 by:

  • including and renaming the BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS for genome and transcriptome
  • defining ch_transcriptome_bai (not sure using this one is correct given original transcript bam used in ch_transcriptome_bam = FASTQ_ALIGN_STAR.out.orig_bam_transcript
  • adding --with_umi param logic to ensure umi_tools prepare-for-rsem deduplicated reads are quantified with Salmon

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/riboseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • 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).

@iraiosub iraiosub self-assigned this Dec 2, 2024
@iraiosub iraiosub mentioned this pull request Dec 2, 2024
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github-actions bot commented Dec 2, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fabee5d

+| ✅ 225 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • files_unchanged - File ignored due to lint config: assets/nf-core-riboseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-riboseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-riboseq_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_ci - actions_ci

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-12-02 22:10:15

@iraiosub iraiosub added the bug Something isn't working label Dec 2, 2024
FelixKrueger
FelixKrueger approved these changes Dec 3, 2024
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That looks fairly straightforward to me. We can give it a go with with some test data after lunch.

@FelixKrueger FelixKrueger merged commit 29e36ea into nf-core:dev Dec 3, 2024
110 checks passed
@iraiosub iraiosub deleted the feat-umi-fix branch December 3, 2024 12:39
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@pinin4fjords pinin4fjords pinin4fjords left review comments

@FelixKrueger FelixKrueger FelixKrueger approved these changes

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@iraiosub @pinin4fjords @FelixKrueger