Simplify configuration file for running deepRVAT #99
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…rvat into simplify-config-files
HolEv
reviewed
May 28, 2024
Simplifying association testing phenotypes .
HolEv
reviewed
May 29, 2024
HolEv
reviewed
May 29, 2024
bfclarke
requested changes
May 29, 2024
bfclarke
reviewed
Jun 1, 2024
…e pipelines -fixed configfile path in annotation pipeline
bfclarke
approved these changes
Jun 24, 2024
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What
Allows users to interact with a deeprvat_input_config.yaml that is a more simplified configuration file with only those parameters most relevant to users. The main deeprvat_config.yaml used for the pipelines is then created automatically based on the input from deeprvat_input_config.yaml, when running a pipeline.
Testing
Testing this PR involved running the various deepRVAT pipelines using the respective
deeprvat_input_config.yaml(see specific pipeline input configs in '/example/config/' ) . Subsequently, then testing all pipeline scripts requiring the generateddeeprvat_config.yamlfile.Instructions
Run your desired training and/or association testing snakemake pipeline, i.e.
training_association_testing.snakefile. The snakemake pipeline expects the generateddeeprvat_config.yamlfile. Ifdeeprvat_config.yamlhas not been previously generated or supplied via the snakemake --configfile argument, then the pipelines expects a 'deeprvat_input_config.yaml' file to be present in the working directory. Then the snakemake pipeline will automatically generate the necessarydeeprvat_config.yamlinto your working directory based on 'deeprvat_input_config.yaml'.