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Added an optional field bam_type to allow simultaneous input of both Subreads and CCS sequences #41

Merged
merged 6 commits into from
Jan 14, 2025
Merged

Added an optional field bam_type to allow simultaneous input of both Subreads and CCS sequences #41

merged 6 commits into from
Jan 14, 2025

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GallVp
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@GallVp GallVp commented Jan 8, 2025

PR checklist

  • Added an optional field bam_type to schema_input to allow simultaneous input of both Subreads and CCS sequences #40
  • 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/isoseq 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>).
  • 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).

@GallVp GallVp requested a review from sguizard January 8, 2025 23:36
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GallVp commented Jan 8, 2025

I guess an update of the nf-core template is also needed. I'll first work on that and then rebase this one.

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github-actions bot commented Jan 13, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5f2bcf2

+| ✅ 192 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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 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!

❔ Tests ignored:

  • files_unchanged - Required pipeline config not found - {'manifest.author'}

✅ Tests passed:

Run details

  • nf-core/tools version 3.1.1
  • Run at 2025-01-13 22:33:37

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GallVp commented Jan 13, 2025

Thank you @sguizard for reviewing the other PR. I think this one is ready for review.

sguizard
sguizard approved these changes Jan 14, 2025
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LGTM
Many thanks for your contributions and this new feature!

@sguizard sguizard mentioned this pull request Jan 14, 2025
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@GallVp GallVp merged commit ba7f569 into nf-core:dev Jan 14, 2025
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@GallVp GallVp deleted the feat/skip_ccs branch January 14, 2025 07:56
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@sguizard sguizard sguizard approved these changes

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@GallVp @sguizard