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Add MetaEuk for Eukaryotic genome annotation#481

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jfy133 merged 10 commits intonf-core:devfrom
prototaxites:metaeuk
Jul 29, 2023
Merged

Add MetaEuk for Eukaryotic genome annotation#481
jfy133 merged 10 commits intonf-core:devfrom
prototaxites:metaeuk

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@prototaxites prototaxites commented Jul 21, 2023 •
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Hope I caught everything but should just work. Will try and update the process diagram sometime next week, but am in the lab so will see where I can squeeze the time in!

@jfy133 Should we squeeze this one into the next release? Happy to wait, but it might be nice to tie domain classification in with a feature to justify its inclusion (beyond making DAS_tool only take prokaryotic bins).

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/mag 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 Jul 21, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 966984b

+| ✅ 156 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ 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 ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-25 07:31:58

jfy133
jfy133 approved these changes Jul 21, 2023
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Yeah I said no more functionality but I'm dragging on and I can see your point about the benefits of including this with the domain classification stuff... but this is the last one for this release!

Comment thread docs/output.md Outdated
Comment thread conf/modules.config
@prototaxites prototaxites requested a review from d4straub July 24, 2023 07:08
jfy133
jfy133 approved these changes Jul 25, 2023
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Comment thread docs/output.md Outdated
Comment thread lib/WorkflowMag.groovy Outdated
prototaxites and others added 2 commits July 25, 2023 08:26
@jfy133 jfy133 merged commit 0d24a2e into nf-core:dev Jul 29, 2023
@prototaxites prototaxites deleted the metaeuk branch August 3, 2023 08:48
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@jfy133 jfy133 jfy133 approved these changes

@d4straub d4straub Awaiting requested review from d4straub d4straub is a code owner

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