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Rationalise sorted bam/bai publishing #85

Merged
merged 6 commits into from
Jan 24, 2025
Merged

Rationalise sorted bam/bai publishing #85

merged 6 commits into from
Jan 24, 2025

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pinin4fjords
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@pinin4fjords pinin4fjords commented Jan 23, 2025 •
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Closes #84

This fixes and somewhat simplifies the publishing of BAMs and BAIs for sorted transcriptome and genome results.

Aslo fixed issues I noticed with publish paths for files after deduplication

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 linked an issue Jan 23, 2025 that may be closed by this pull request
Transcriptome Index does not get published #84
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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 Jan 23, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 24514c0

+| ✅ 232 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 2025-01-23 18:30:15

FelixKrueger
FelixKrueger approved these changes Jan 23, 2025
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@FelixKrueger FelixKrueger left a comment

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Thanks very much!

@pinin4fjords pinin4fjords merged commit 6ba925f into dev Jan 24, 2025
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@pinin4fjords pinin4fjords deleted the fix_simplify_index_publishing branch January 24, 2025 09:15
@pinin4fjords pinin4fjords mentioned this pull request Jan 30, 2025
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@FelixKrueger FelixKrueger FelixKrueger approved these changes

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Transcriptome Index does not get published
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@pinin4fjords @nf-core-bot @FelixKrueger