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Add skani round 2 #5539

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Add skani round 2 #5539

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CarsonJM
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PR checklist

Re-opens #5502

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@CarsonJM CarsonJM requested a review from a team as a code owner April 29, 2024 21:12
@CarsonJM CarsonJM requested review from Aratz and removed request for a team April 29, 2024 21:12
@CarsonJM
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@jfy133 back in action part2. I'm still experimenting with the best way to add the -l option, but will let you know when I'm ready for another review!

nvnieuwk
nvnieuwk approved these changes May 7, 2024
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LGTM (just some small comments)

It's also advised to only add one module per PR, I know it's easier to add multiple in the same PR (been there, done that), but no one really wants to review a large PR 😁

modules/nf-core/skani/dist/meta.yml
description: |
FASTA/skani sketch file to be used as query.
pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,sketch}"
- reference:
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Can you add meta2 here too?

modules/nf-core/skani/search/meta.yml
description: |
Input FASTA/skani sketch to search with.
pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}"
- sketch_dir:
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Same here

modules/nf-core/skani/triangle/main.nf
'biocontainers/skani:0.2.1--h4ac6f70_0' }"

input:
tuple val(meta) , path(queries)
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Suggested change
tuple val(meta) , path(queries)
tuple val(meta), path(queries)

@SPPearce
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@CarsonJM , can you make the adjustments suggested here?

@CarsonJM
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Yes I can! I am in the middle of a wet-lab onslaught at the moment and have fallen behind on nf-core stuff, but am hoping to be back at it soon!

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@nvnieuwk nvnieuwk nvnieuwk approved these changes

@Aratz Aratz Awaiting requested review from Aratz Aratz is a code owner automatically assigned from nf-core/nf-test

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@CarsonJM @SPPearce @nvnieuwk