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Include sizes in samtools faidx #7041

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@maxulysse maxulysse commented Nov 20, 2024

Long term plan of wold domination converging modules in between sarek and rnaseq.
Get rid of custom/getchromsizes and put it in samtools/faidx with a boolean.

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!
  • 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.
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Think the number of tests here is a bit excessive now.

- - get_sizes:
type: boolean
description: use cut to get the sizes of the index (true) or not (false)
pattern: "true or false"
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Is this really how we specify a boolean?

@@ -71,10 +87,17 @@ output:
description: File containing software versions
pattern: "versions.yml"
authors:
- "@chris-cheshire"
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Don't think we need all these authors and maintainers...

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3 participants