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Run CAT on unbinnned contigs as well as binned contigs #385

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merged 1 commit into from
Jan 31, 2023
Merged

Run CAT on unbinnned contigs as well as binned contigs #385

merged 1 commit into from
Jan 31, 2023

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jfy133
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@jfy133 jfy133 commented Jan 30, 2023

Closes #125

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  • This comment contains a description of changes (with reason).
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@jfy133 jfy133 requested review from d4straub and skrakau and removed request for d4straub January 30, 2023 09:51
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github-actions bot commented Jan 30, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a119556

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

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered 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 2.7.2
  • Run at 2023-01-30 09:53:32

@jfy133 jfy133 linked an issue Jan 30, 2023 that may be closed by this pull request
Apply CAT also on unbinned contigs #125
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Did you test that? Maybe I misunderstood, but doesnt your change mean that also all unbinned contigs (potentially millions) are classified by CAT? If I am right, CAT will be unusable for larger (and not very well assembled & binned) assemblies because it will take around >=1000x longer. This would need to be optional or only contigs above a specific length threshold (that would be adjustable) or such.

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jfy133 commented Jan 31, 2023 •
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Did you test that? Maybe I misunderstood, but doesnt your change mean that also all unbinned contigs (potentially millions) are classified by CAT? If I am right, CAT will be unusable for larger (and not very well assembled & binned) assemblies because it will take around >=1000x longer. This would need to be optional or only contigs above a specific length threshold (that would be adjustable) or such.

On the test data yes, not on real data (I dont have any at hand). Note that the 'unbinned' here means the contigs considered 'OK' from split_fasta, so there is a certain level of filtering going on there. It's not just any random contig.

I could make it optional, but maybe it would be to discuss on #125 then before I continue, if this is not sufficient?

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I see, thanks, I didnt make the connection! Indeed, then "only" contigs that are above --min_length_unbinned_contigs are added, i.e. by default >=1.000.000 bp, that seems good!

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LGTM!

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jfy133 commented Jan 31, 2023

I see, thanks, I didnt make the connection! Indeed, then "only" contigs that are above --min_length_unbinned_contigs are added, i.e. by default >=1.000.000 bp, that seems good!

Correct! Basically the same input for e.g. BUSCO and other dowsntream tools :)

@jfy133 jfy133 merged commit cd91bc5 into dev Jan 31, 2023
@jfy133 jfy133 deleted the cat-unbinnned branch January 31, 2023 11:39
@jfy133 jfy133 mentioned this pull request Feb 27, 2023
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@d4straub d4straub d4straub approved these changes

@skrakau skrakau Awaiting requested review from skrakau

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Apply CAT also on unbinned contigs
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