Clinical-Genomics
1.0.0
develop1.0.0
1.0.0
develop1.0.0
  • Introduction
  • Documentation
    • Setup
    • References
    • Analysis
    • Parameters
    • Recipes
    • Code
      • Best Practise
      • Adding an env
    • API
      • Define Parameters
      • Download References
      • Identifiers
      • Initiation File
      • Install
      • IO
      • Modules
      • Path
      • Pedigree
      • QC metrics
      • Sample info
      • Tests
        • Log
        • Data
      • Subroutines
    • Cli
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  1. Documentation

References

PreviousSetupNextAnalysis

Last updated 3 years ago

MIP can download many program prerequisites automatically via the mip download application mip download. Each pipeline has a yaml file where available references are specified (, [rdrna]((-1.0-.yaml)) and the API is described .

To download the references using MIP, run:

$ mip download --reference_dir <reference_dir> --config <download_config>

This will submit SLURM jobs that automatically downloads all references specified in the config that is not already present in the reference directory.

For a full list of download options, run:

$ mip download --help

Updating a reference

Open the download config corresponding to your pipeline and update or add a new version_tag in the reference hash. Update the same version tag together with any metadata changes in the reference_feature hash, see the API for details. Run the same mip command as above to download your updated reference.

To include the changes in the analysis - add your reference to your mip config.yaml file where appropriate.

rd_dna
https://github.com/Clinical-Genomics/MIP/blob/develop/templates/mip_download_rd_rna_config
here