pypiper
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databio
Python toolkit for building restartable pipelines
Homogenization seems to be such a :fire: theme right now. Anyway... It'd be nice to bring the signatures for the peak caller functions into closer alignment. There's a slight discrepancy...
Since NGSTk offers--nominally and substantively--a toolkit of NGS functions, it seems like there's intent to have users be able to treat it as a collection of general-purpose functions, maybe in...
Total chromosome sizes are hardcoded in the function "macs2CallPeaksATACSeq" and "macs2CallPeaks" of ngstk.py. So I ran into problems when I did the analysis with mm9. Maybe this could be added...
I was running two pipelines in the same directory/sample and when one finished, it noticed the flag of the other (even though it is named diferently) and did not clean...
It seems like a pipeline may run many--often, maybe even all--commands within a container if one is in use. Should we consider making use of a `PipelineManager`'s container the default...
Raised in discussion with @j-lawson How do `ngstk` functions handle pass-filter reads? At the moment it looks like they are passed on and not changed. we should probably add a...
https://github.com/epigen/pypiper/issues/48 > I've been thinking about this. Background: That function is not used anywhere within pypiper. It's only used (apparently) in this pipeline (or maybe some others). My thoughts: I...
The calculate_frip command in ngstk.py calculates FrIP as the sum of the 5th column of the sambamba detph command. However the sambamba command outputs the original bed file adding its...
Currently, pypiper output files start with the pipeline name and then the file type, like PIPE_log.md and PIPE_profile.md, etc. (see [docs](http://pypiper.readthedocs.io/en/latest/outputs.html)) I did it this way to make it so...