When using an external junction reads file, copy to outrigger_output folder

[olgabot]

Description

When using an external junction reads file with --junction-reads-csv, then the original file is still wherever else in the filesystem it is, and since storage is cheap and to be consistent with the other implementations, this file should be copied over to outrigger_output/junctions/reads.csv

For example, I'm running outrigger now and have this folder as my output so far:

(outrigger_v1.0.0rc1) [obotvinnik@tscc-login2 analysis]$ tree outrigger_v2/
outrigger_v2/
├── index
│   └── gtf
│       ├── gencode.v19.annotation.gtf.db
│       └── gencode.v19.annotation.gtf.db-journal
└── junctions
    └── metadata.csv

3 directories, 3 files

But now I have to go back and hunt down which were the actual reads that were used in this analysis.