Merge BBN bowtie2 branch

emyounglab / prymetime

Pipeline for Recombinant Yeast genoMEs That Identifies Markers of Engineering

MIT License

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Closed tyler-e-marshall closed 2 years ago

tyler-e-marshall commented 2 years ago

The main change is replacing instances of minimap2 with bowtie2.

Other changes:

Increasing default JVM heap space for pilon
Enabling multi threading on most tools. An option to prymetime was added, and the default is 8. I chose 8 because it was already being used for some tools that had threading on by default.