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eriqande / mega-post-bcf-exploratory-snakeflows

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Consider putting bcf information into the config.yaml rather than the harder to read TSV #4

Open eriqande opened 2 years ago

eriqande commented 2 years ago

It would go something like this:

bcf_list:
    id: TEST-Biallelic-SNPS-5-fish-maf-0.1
        path:  .test/bcf/test.bcf
        sample_subset_path: .test/config/sample_subsets/fish5.txt
        bcftools_opts:  -v snps -m 2 -M 2 -i 
        scaff_group_path: .test/bcf/test.bcf.scaff_groups.tsv
    id: The-next-one-to-use
        path:  etc.

I think that would be a lot easier to look at and modify, etc.

eriqande commented 2 years ago

This would definitely be the way to do this, I think. And then we could have some other sections for each one that defined the MAFs that we wanted, and other things. (Those could be defined as lists). Then we could expand those into the appropriate paths in a rule all.

eriqande commented 2 years ago

I am not going to get moving on this until I have finished up the Yukon association study (quick and dirty). But once that is done, I am going to prioritize cleaning this up.