Update docs and minor code fixes

harvardinformatics / snpArcher

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.

MIT License

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Closed tsackton closed 1 year ago

tsackton commented 1 year ago

This PR updates the README, and also:

revises write_samples.py to create refPath in the sample sheet, and also optionally use a NCBI accession instead of a local reference, in the case where you have local fastqs being mapped to a published genome
adds resources to some qc steps, and adds minor bugfixes in a few places