v3.0.0-alpha

This is the initial alpha release of the ENCODE DNase-seq pipeline. It is functionally similar to our old DNAnexus pipeline (https://github.com/ENCODE-DCC/dnase_pipeline/) but has been entirely rewritten in our reproducible WDL/Caper/Cromwell/Docker/testing framework. All tasks, subworkflows, and workflows have unit, integration, and functional tests, respectively. While many of the outputs and QC are similar we are additionally outputting 0.1% Hotspot2 peaks and 1% FDR footprints. It is based on the pipeline implemented by the Stam Lab in the stampipes repo (https://github.com/StamLab/stampipes).