TODO

TODOs for project:

# project_config management

Consider splitting project_config into two parts:
* `project_config_host`
  * Defines all host paths
  * project name
  * Expected to vary per analysis project
  * Visible prior to `docker run`
* `project_config_container`
  * defines all container paths
  * Visible within container
  * expected to change with BICSEQ2 development


# Pipeline improvements

## Detect memory issues
* Maybe move away from parallel to bsub, it will detect better if there is memory problem or find ways to have parallel to report memory issues

## Disk Space usage
```
Here is disk space usage for chr 20-23:
    640K    bed
    129M    norm
    320K    segmentation
    995M    unique_reads
```

### unique_reads:
```
-rw-r--r-- 1 mwyczalk dinglab  375 Jan  9 12:53 C3L-00001.WGS.N.hg38.chr18.get_uniq.log
-rw-r--r-- 1 mwyczalk dinglab  45M Jan  9 12:53 C3L-00001.WGS.N.hg38_chr18.seq.gz
-rw-r--r-- 1 mwyczalk dinglab  375 Jan  9 12:52 C3L-00001.WGS.N.hg38.chr19.get_uniq.log
-rw-r--r-- 1 mwyczalk dinglab 147M Jan  9 12:52 C3L-00001.WGS.N.hg38_chr19.seq
-rw-r--r-- 1 mwyczalk dinglab  375 Jan  9 12:53 C3L-00001.WGS.N.hg38.chr20.get_uniq.log
-rw-r--r-- 1 mwyczalk dinglab 171M Jan  9 12:53 C3L-00001.WGS.N.hg38_chr20.seq
-rw-r--r-- 1 mwyczalk dinglab  375 Jan  9 12:50 C3L-00001.WGS.T.hg38.chr18.get_uniq.log
```

Compressing unique_reads is quite effective:
```
C3L-00001.WGS.N.hg38_chr18.seq:  78.2% -- replaced with C3L-00001.WGS.N.hg38_chr18.seq.gz
```

### norm:
```
-rw-r--r-- 1 mwyczalk dinglab 26M Jan  9 13:05 C3L-00001.WGS.N.hg38.chr18.norm.bin
-rw-r--r-- 1 mwyczalk dinglab 19M Jan  9 13:06 C3L-00001.WGS.N.hg38.chr19.norm.bin
-rw-r--r-- 1 mwyczalk dinglab 21M Jan  9 13:07 C3L-00001.WGS.N.hg38.chr20.norm.bin
-rw-r--r-- 1 mwyczalk dinglab 772 Jan  9 13:00 C3L-00001.WGS.N.hg38.norm-config.txt
-rw-r--r-- 1 mwyczalk dinglab 66K Jan  9 13:07 C3L-00001.WGS.N.hg38.out.txt
```

compression:
```
C3L-00001.WGS.N.hg38.chr18.norm.bin:     66.2% -- replaced with C3L-00001.WGS.N.hg38.chr18.norm.bin.gz
```