add support for mixed local and sra fastqs

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 cademirch closed 6 months ago

cademirch commented 6 months ago

Add support for mixed local file and sra fastqs in sample sheet - #145

modified get_reads to check if fq1 and fq2 are null for a given sample, if so then try to download via sra
added test case in ecoli tests