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Ribotricer orf prediction #40

Merged
merged 23 commits into from
Apr 3, 2024
Merged

Ribotricer orf prediction #40

merged 23 commits into from
Apr 3, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Mar 18, 2024 •
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This PR adds ORF prediction with Ribotricer.

Unfortunately, Ribotricer won't run in the test profile due to hard limits on read coverage. I opened an issue and PR in Ribotricer to try to address this.

I'm also verifying that it will run with full-size test data, with the test_full profile.

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 (nextflow run . -profile 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).

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github-actions bot commented Mar 18, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 05cdad2

+| ✅ 186 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  10 tests had warnings |!

❗ 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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 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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • schema_description - No description provided in schema for parameter: skip_ribotricer

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-03 09:45:57

This was linked to issues Mar 19, 2024
Add ribotricer detectorfs module #19
Closed
Add ribotricer/prepareorfs #18
Closed
@pinin4fjords pinin4fjords requested a review from maxulysse April 3, 2024 09:47
@pinin4fjords pinin4fjords merged commit 5ae9054 into dev Apr 3, 2024
97 checks passed
@pinin4fjords pinin4fjords deleted the ribotricer_orf_prediction branch April 3, 2024 10:22
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@maxulysse maxulysse maxulysse approved these changes

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Add ribotricer detectorfs module Add ribotricer/prepareorfs
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