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limey-bean / Anacapa

Written by Emily Curd (eecurd@g.ucla.edu), Jesse Gomer (jessegomer@gmail.com), Gaurav Kandlikar (gkandlikar@ucla.edu), Zack Gold (zjgold@ucla.edu), Max Ogden (max@maxogden.com), Lenore Pipes (lpipes@berkeley.edu)and Baochen Shi (biosbc@gmail.com). Assistance was provided by Rachel Meyer (rsmeyer@ucla.edu).
MIT License
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Dada2 unified script #24

Closed gauravsk closed 6 years ago

gauravsk commented 6 years ago

Emily, you can test this on other datasets using the following:

Rscript --vanilla dada2_unified_script.R "BAT16S" "/u/home/g/gaurav/bat_test/" 120  "paired"
Rscript --vanilla dada2_unified_script.R "BAT16S" "/u/home/g/gaurav/bat_test/" 120  "forward"
Rscript --vanilla dada2_unified_script.R "BAT16S" "/u/home/g/gaurav/bat_test/" 120  "reverse"

I also added in some lines to create directories from within R which should simplify the structure of the job submission shell script but we can chat later. I also added a few extra checks within the script to break it if things are going poorly.