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Minimal workflow requirements #2

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8 of 13 tasks
lauraporta opened this issue Dec 4, 2024 · 0 comments
Open
8 of 13 tasks

Minimal workflow requirements #2

lauraporta opened this issue Dec 4, 2024 · 0 comments

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@lauraporta
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lauraporta commented Dec 4, 2024 •
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I'm building a Snakemake workflow in dev and I want it to have some features before being committed to main in the #1 PR.

A tentative list of features (might not be all present in the first version):

  • A setup rule
  • A preprocessing rule
  • Slurm processing
  • Infer the number of slurm jobs to run depending on number of datasets - can do a dry run first to count them
  • All rules need to depend on setup No setup needed anymore
  • Structure the projects for methods and metrics couples
  • Preprocessing needs to be flexible in the methods and metrics it accepts
  • Config file in which to set up custom paths and parameters for snakemake
  • Do I still need Reader and Writer classes? Can the scripts be simplified with the usage of wildcards? -> Deleted, using wildcards
  • Generate small report
  • Figure out the command to generate simple dashboard (with datavzrd?) from reports (to visualise the metrics)
  • Snakemake tests
  • README with project description and usage explanation
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@lauraporta