Jason Smith

#### Regarding "Connection to CWL" 1: It seems that a simple, or more straightforward, approach is simply to eliminate the special status of `required_assets` and subsume them into just parameters,...

A couple challenges I've dealt with so far and worth keeping track of are listed here. I'm also not sure how much of this would be modifiable based on the...

Potential fix, although it's performing the sambamba step twice, so to speak; but should be flexible to differing column numbers from the input bed. `def calculate_frip(self, input_bam, input_bed, output, cpus=4):`...

Yeah, that works. I honestly didn't even think of that. Only issue there is if sambamba ever changes location of its readCount column? Im assuming you're saying take column 5...

I had thought of that, but was avoiding trying to have another temp file to delete, if that is a concern...

Yes. you're likely right. Also, could use `cut -f 1-3 {}.format(input_bed)` and therefore the readCount column is always column 4. But that still requires a temporary file. So far, `ngstk.py`...