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Update MaxBin2: allow multiple abund files #6776

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merged 3 commits into from
Oct 14, 2024

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d4straub
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Currently this modules allows the input of only one abundance file with one abundance column. This adds a possibility to use multiple abundance files (each with the contig abundance of one sample).
Related to nf-core/mag#690

PR checklist

Closes #XXX

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
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@d4straub d4straub requested a review from jfy133 October 14, 2024 07:09
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Interesting, the problem is "modules/nf-core/maxbin2/meta.yml::$.input[0][3].abund.type: 'file or list of files' is not one of ['map', 'file', 'directory', 'string', 'integer', 'float', 'boolean', 'list']", so when I accept a file or a list of files, how shall I write that here? :D

@jfy133 jfy133 changed the title allow multiple abund files Update MaxBin2: allow multiple abund files Oct 14, 2024
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jfy133 commented Oct 14, 2024

Interesting, the problem is "modules/nf-core/maxbin2/meta.yml::$.input[0][3].abund.type: 'file or list of files' is not one of ['map', 'file', 'directory', 'string', 'integer', 'float', 'boolean', 'list']", so when I accept a file or a list of files, how shall I write that here? :D

I would say a list a list of one file is still technically a list 😬

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Hm, but according to groovy, abund instanceof List is false for one file, true for multiple. But if you are fine with list then I am as well!

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jfy133 commented Oct 14, 2024

@nf-core-bot fix linting

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Nothing for me to do here! 🤷
This is probably because the linting errors come from nf-core lint and have to be fixed manually (or with nf-core lint --fix).

Co-authored-by: James A. Fellows Yates <[email protected]>
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jfy133 commented Oct 14, 2024

Hm, but according to groovy, abund instanceof List is false for one file, true for multiple. But if you are fine with list then I am as well!

Yeah but the meta.yaml is not used for anything, more for documenting, and I would rather go for the more complex input for clarity

Co-authored-by: James A. Fellows Yates <[email protected]>
@jfy133 jfy133 added this pull request to the merge queue Oct 14, 2024
Merged via the queue into nf-core:master with commit 2836131 Oct 14, 2024
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2 participants