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RNA detection for genomes_submit#23

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KateSakharova merged 3 commits intodevfrom
feature/rna_detection
Mar 11, 2026
Merged

RNA detection for genomes_submit#23
KateSakharova merged 3 commits intodevfrom
feature/rna_detection

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@KateSakharova KateSakharova commented Oct 29, 2025 •
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RNA part works. Upload will be added in separate PR
Tests also would be in the end of flow development

Resolving #10

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/seqsubmit branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,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).

@KateSakharova KateSakharova changed the title WIP RNA detection for genomes_submit Oct 29, 2025
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nf-core-bot commented Mar 10, 2026 •
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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: 3.5.1.
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.

@KateSakharova KateSakharova force-pushed the feature/rna_detection branch from d1169f1 to bac5af3 Compare March 10, 2026 21:08
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github-actions bot commented Mar 10, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e2843f4

+| ✅ 199 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  24 tests had warnings |!
Details

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • 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 nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in test_assembly.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test_assembly.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_genome.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test_genome.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in environment.yml: List required Conda package(s).
  • pipeline_todos - TODO string in main.nf.test: Once you have added the required tests, please run the following command to build this file:
  • 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!
  • local_component_structure - rna_detection.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • nextflow_config - Config variable ignored: params.input
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-seqsubmit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-seqsubmit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-seqsubmit_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-03-11 12:52:02

@KateSakharova KateSakharova marked this pull request as ready for review March 11, 2026 11:34
mberacochea
mberacochea approved these changes Mar 11, 2026
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Thanks @KateSakharova .. this is still WIP so we will fix the checks in a bit.

@KateSakharova KateSakharova force-pushed the feature/rna_detection branch from 6be6c35 to e2843f4 Compare March 11, 2026 12:50
@KateSakharova KateSakharova merged commit f904453 into dev Mar 11, 2026
10 of 16 checks passed
@KateSakharova KateSakharova deleted the feature/rna_detection branch March 11, 2026 12:52
@KateSakharova KateSakharova mentioned this pull request Mar 11, 2026
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@mberacochea mberacochea mberacochea approved these changes

@vagkaratzas vagkaratzas Awaiting requested review from vagkaratzas

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