Nathan Sheffield

probably this would be better to put as an option to `PipelineManager` so the author could state *which* pipelines to consider, or whether to consider none at all, when deciding...

~what do you mean it's performing the sambamba step twice? it only returns `cmd2`...~ I see now that `cmd2` runs `cmd1` two times... But why not just calculate the number...

yeah. Or why not just run the command once, and then run `head` on the outfile to get the readCount column and use that?

Yeah I guess that's a concern...but I feel more concerned about running the thing twice. It can potentially be a long step, right?

@afrendeiro I think you wrote the original `calculate_frip` function -- did you have any comment on this?

Ok, the advantage is only relevant if you are going through output files a lot, which you may not do, but I do. The disruption would just be if scripts...

Well, if anyone has examples of scripts that rely on this naming scheme, let us know. The only one I can think of is the checks for the flags, which...

of course, but I think you're missing the point... I'm just talking about looking at a single sample, and saving the split second of an extra tab-completion step, because everything...

One issue: re-runs of a currently completed pipeline would re-run everything one time because they wouldn't find the new complete flag name.

I think I will go ahead with it but leave the flag files unchanged, so it shouldn't disrupt anything. If anyone feels strongly that this is a bad idea, speak...