update logic to handle multiple data files as input for reads qc

[aclum]

Berkeley schema will allow for multiple runs from the same library which will be analyzed together. This will break the assumptions embedded about how to handle an array of length 1 or > 2. The code currently assumes that if length=1 then the file is interleaved and if it is > 1 it is not. We need to update the wdl/input.json such that it could handle the following use cases:
1 interleaved file
1+n interleaved files
2 files, one for read 1 & one for read 2
2+n(even only)

My suggestion for how to handle this is to update the format of the input json
to look something like this

rqcfilter.input_files:[{'interleaved':"interleaved_1.fastq.gz"},{'interleaved':"interleaved_1.fastq.gz"}]
rqcfilter.input_files:[{"read_1":"interleaved_1_R1.fastq.gz","read_2":"interleaved_1_R1.fastq.gz"},{:read_1":"interleaved_2_R1.fastq.gz","read_2":"interleaved_2_R1.fastq.gz"}]