sjswuitchik
commented
3 years ago - added bzip2 dependency for bedtools to work efficiently with compressed VCF (envs/bam2vcf.yml)
- sortVcf rule added before vcftools and bedtools rules for less memory usage (bam2vcf_fb and bam2vcf_gatk)
- rewrote intervals creation function to remedy list0 duplication (helperFun.py)
- added resource requests for multiple rules (resources.yaml)
- removed duplicated resource requests for bam2vcf workflows because freebayes resources were same name/request as gatk resources (resources.yaml)
- split and re-ordered GATK gatherVcfs rule into filterVcfs, gatherVcfs, and sortVcf (bam2vcf_fb and bam2vcf_gatk)
- changed SNPs per interval calculation from bedtools intersect to bedtools coverage for increased efficiency (bam2vcf_fb and bam2vcf_gatk)