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feat: Add vg giraffe #3302

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feat: Add vg giraffe #3302

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FelixMoelder
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@FelixMoelder FelixMoelder commented Oct 16, 2024

This adds vg giraffe for mapping reads as bam records.
Like for bwa mem sorting reads by samtools, picard or fgbio is supported.

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While the contributions guidelines are more extensive, please particularly ensure that:

  • test.py was updated to call any added or updated example rules in a Snakefile
  • input: and output: file paths in the rules can be chosen arbitrarily
  • wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:)
  • temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to
  • the meta.yaml contains a link to the documentation of the respective tool or command under url:
  • conda environments use a minimal amount of channels and packages, in recommended ordering

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