core number calculation needs to force an int result (python3)

databio / pepatac

A modular, containerized pipeline for ATAC-seq data processing

http://pepatac.databio.org

BSD 2-Clause "Simplified" License

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Closed stolarczyk closed 5 years ago

stolarczyk commented 5 years ago

in bamSitesToWig.py call the cores calculation fails to produce an integer when running with python 3 and the pipeline fails every time:

bamSitesToWig.py: error: argument -p/--cores: invalid int value: '5.333333333333333'

nsheff commented 5 years ago

this was fixed in a4ecd1910c8f59afa8344ba471ad820591f7bd76

dimkonstanto commented 5 years ago

The code is still "cmd += " -p " + str(max(1, int(pm.cores) * 2/3)) " in the most recent pepatac.py script downloaded by github.