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tjbencomo / ngs-pipeline

Pipeline for Somatic Variant Calling with WES and WGS data
MIT License
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Implement changes from test run #33

Closed tjbencomo closed 4 years ago

tjbencomo commented 4 years ago
  1. Set vep, vcf2maf, and concat_mafs to be local rules
  2. Increase FastQC and multiqc times in cluster-config.json
tjbencomo commented 4 years ago

Decided to leave rules from 1) as normal rules because with several patients (20+), it will be slow to process all of them sequentially

tjbencomo commented 4 years ago

Might as well remove environment.yml as I no longer use one environment with all the executables but smaller environments depending on the rule being called