added -extra_param_bwt2 for bowtie2
added -extra_param_bwt2 for bowtie2

kundajelab/atac_dnase_pipelines,kundajelab/atac_dnase_pipelines,kundajelab/atac_dnase_pipelines,kundajelab/atac_dnase_pipelines,kundajelab/atac_dnase_pipelines