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Snakemake #45

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pommevilla opened this issue Jan 11, 2023 · 0 comments
Open

Snakemake #45

pommevilla opened this issue Jan 11, 2023 · 0 comments
Milestone
v2.0

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@pommevilla
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pommevilla commented Jan 11, 2023 •
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Convert to a Snakemake pipeline. There should be a rules/mfp<step> file for each of the commands that currently exist in the pipeline.

User stories

  • As a user, I want to be able to choose to run this on my local computer and not have to use Slurm
  • As a user, I want to be able to choose between running the whole pipeline and running individual steps

Questions

  • What are the targets?
  • What are the inputs?
  • What are the intermediate files?
  • How can we make it so the user can run just part of the pipeline at a time?
    • Perhaps sending the commands to a Docker container which runs the desired step?
@pommevilla pommevilla added this to the v2.0 milestone Jan 11, 2023
@pommevilla pommevilla mentioned this issue Jan 11, 2023
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45-snakemake pommevilla/MetaFunPrimer
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