Refactor intervals and bug fixes for fastq2bam

harvardinformatics / snpArcher

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

MIT License

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Refactor intervals and bug fixes for fastq2bam #4

Closed cademirch closed 2 years ago

cademirch commented 2 years ago

Refactored intervals and corresponding helper functions for using samples sheet. Also bug fixes for fastq2bam: added env spec for merge_bams rule, and added cat command for downloading large datasets.