#32 updating logic for reads qc

[vlilanl]

I updated the input.json so that if there are multiple already interleaved files, they go into rqcfilter.input_files. If the files are not interleaved, Read 1 will be placed in rqcfilter.input_fq1 and Read 2 will be placed in rqcfilter.input_fq2. I have also added a boolean to say whether or not the files are interleaved.

This was tested on JAWS.
Interleaved test of 1 : 83296
Interleaved test of 2 : 83295
Not interleaved test of 2 files(1 interleaved file) : 83439
Not interleaved test of 4 files(2 interleaved files) : 83447

[aclum]

@vlilanl at least 83296 doesnt appear to correctly run the finish_rqc to generate the final files.

[vlilanl]

New tests on jaws:
Interleaved test of 1 : 83868
Interleaved test of 2 : 83870
Not interleaved test of 2 files(1 interleaved file) : 83942
Not interleaved test of 4 files(2 interleaved files) : 83943

@kaijli mentioned that there might be potential memory risks later on especially if the input files are large. She recommends that we update the memory to how she did it in metat.

[vlilanl]

Jaws test for increased memory: 84325