data/singleEnd/configFile

doc/ENCODE standards.odt

doc/Ivan_Flowchart_pipeline.odg

doc/TODO

doc/config.json.README

example/NEW/cluster.json

example/NEW/config.json

example/NEW/params.sh

example/NEW/runSnakefile.sh

example/NEW/sampleTableATAC.tsv

example/input/cluster.json

.../input/config (carnold's conflicted copy 2017-03-08).json

example/input/config.json

example/input/params.sh

example/input/test1_rep1_1

src/R/functions.R

src/R/runPipeline.R

src/R/runQC.R

src/Snakemake/.dropbox.attr

src/Snakemake/Snakefile