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Stop prokka from renaming contigs by default #306

Merged
merged 11 commits into from
Aug 31, 2023
Merged

Stop prokka from renaming contigs by default #306

merged 11 commits into from
Aug 31, 2023

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Darcy220606
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PR checklist

This PR closes this issue #305

  • 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/funcscan 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).

@Darcy220606 Darcy220606 requested a review from a team August 22, 2023 09:34
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github-actions bot commented Aug 22, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fea43ba

+| ✅ 157 tests passed       |+
!| ❗   1 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-30 13:26:30

louperelo
louperelo approved these changes Aug 23, 2023
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Looks good to me.
Can this have implications on downstream output names, when tools use the PROKKA annotations? For the summary tools maybe?

@Darcy220606
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Darcy220606 commented Aug 23, 2023 •
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Looks good to me. Can this have implications on downstream output names, when tools use the PROKKA annotations? For the summary tools maybe?

Yes, it does @louperelo. Found it out when i was running the benchmarking with prokka. In the summary tables i got different contig names that were not comparable to those when i ran bakta or prodigal. To fix this issue, i added this parametre to retain the contig names. But theres a catch. Prokka gets confused when the contig name is overly long (i.e. it combines the coverage and lengths of contigs in the LOCUS in gbk) and then antismash raises an error, therefore, this parametre is by default turned off.

By default if annotaion tool is PROKKA, it changes the contig names to PROKKA_#. So if you have short contig names as input, prokka and antismash should not raise an error if the original contigs are retained.

jfy133
jfy133 reviewed Aug 25, 2023
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I swear we went through loops on this and not doing what we already do broke one of the tools..

But making it optional still works 👍

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@Darcy220606 Darcy220606 merged commit e0635da into nf-core:dev Aug 31, 2023
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@Darcy220606 @jfy133 @louperelo @jasmezz