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Move UMI handling to subworkflow, update modules and subworkflows, deal with docs and config fallout #79

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merged 24 commits into from
Dec 20, 2024
Merged

Move UMI handling to subworkflow, update modules and subworkflows, deal with docs and config fallout #79

merged 24 commits into from
Dec 20, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Dec 12, 2024 •
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This is the equivalent of nf-core/rnaseq#1466 in rnaseq, moving umi handling to a subworkflow.

Will need some documentation updates and new parameters, since the subworkflow allows use of umicollapse as an option.

There's also a renaming of the rnaseq preprocessing subworkflow (it's now fastq_qc_trim_filter_setstrandedness), and the associated update brings us fq lint, which is handy.

Also update STAR modules to pull in this modules PR with this fix to this problem.

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).

@pinin4fjords pinin4fjords marked this pull request as draft December 12, 2024 18:24
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Dec 12, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ef575c4

+| ✅ 233 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 2024-12-20 17:41:06

FelixKrueger
FelixKrueger approved these changes Dec 19, 2024
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great, thanks

@pinin4fjords pinin4fjords changed the title Starting point for moving umi handling to nf-core subworkflow Move UMI handling to subworkflow, update modules and subworkflows, deal with docs and config fallout Dec 20, 2024
@pinin4fjords pinin4fjords marked this pull request as ready for review December 20, 2024 17:39
@pinin4fjords pinin4fjords merged commit b40e2ce into dev Dec 20, 2024
114 of 116 checks passed
@FelixKrueger FelixKrueger deleted the umi_handling_from_subworkflow branch January 24, 2025 11:56
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@FelixKrueger FelixKrueger FelixKrueger approved these changes

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