Digital microfluidic biochips have emerged as a popular alternative for laboratory experiments. Pin-count reduction and cross-contamination avoidance are key design considerations for practical applications with different droplets being transported and manipulated on highly integrated biochips. This paper presents the first design automation flow that considers the cross-contamination problems on pin-constrained biochips. The factors that make the problems harder on pin-constrained biochips are explored. To cope with these cross contaminations, this paper proposes: 1) early crossing minimization algorithms during placement, and 2) systematic wash droplet scheduling and routing that require only one extra control pin and zero assay completion time overhead for practical bioassays. Experimental results show the effectiveness and scalability of our algorithms for practical bioassays.