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Fix long reads polishing input channel and refactor long reads polishing section #169

Merged
merged 6 commits into from
Sep 28, 2024
Merged

Fix long reads polishing input channel and refactor long reads polishing section #169

merged 6 commits into from
Sep 28, 2024

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Daniel-VM
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@Daniel-VM Daniel-VM commented Sep 18, 2024 •
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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/bacass 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).

PR Description

This PR fixes a wrong channel input for MINIMAP_ALIGN module (#165 )

The logic for long read polishing has been updated as follows:

  • Long read polishing is now restricted to assembly_type == long (hybrid mode uses different tools and a separate polishing strategy).
  • Fixed: The polished genome from the long reads (assembly_type == long) is now the default candidate for downstream analysis.

(Closes #165 )

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

Posted for pipeline commit 0917bda

+| ✅ 198 tests passed       |+
#| ❔   2 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-23 07:22:35

@Daniel-VM Daniel-VM marked this pull request as ready for review September 23, 2024 14:23
charles-plessy
charles-plessy approved these changes Sep 27, 2024
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Looks good to me!

@Daniel-VM Daniel-VM merged commit 3f6a42d into nf-core:dev Sep 28, 2024
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Thanks @charles-plessy :)

@Daniel-VM Daniel-VM mentioned this pull request Oct 1, 2024
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@charles-plessy charles-plessy charles-plessy approved these changes

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@Daniel-VM @charles-plessy