Adds a new Stage - create a custom config for each run of the pipeline (incorporating content specific to the Cohort & sequencing type). Instead of putting everything into the config for every run, then selecting out the bits relevant to this run, create a specific config file for this run.
This separation means that the config for a given Talos run is much easier to define (which will aid redeployment at other sites where the CPG config structure isn't used by default).
This config file is stored in the main output folder for posterity.
Adds a new Stage - create a custom config for each run of the pipeline (incorporating content specific to the Cohort & sequencing type). Instead of putting everything into the config for every run, then selecting out the bits relevant to this run, create a specific config file for this run.
This separation means that the config for a given Talos run is much easier to define (which will aid redeployment at other sites where the CPG config structure isn't used by default).
This config file is stored in the main output folder for posterity.
Linked with https://github.com/populationgenomics/automated-interpretation-pipeline/pull/416