pipeConfigure2

This function is used for setting Configures.

Note

This function is designed for case control comparison.

Parameters

pipeConfigure2(threads=(cpu_count() / 2), genome=None, refdir=None, outdir=None,
               data=None, type=None, case=None, ctrl=None, build=False,)

• threads: int, how many thread to use, default: 1. Do not use the entire computational resources.

• genome: str, which genome you want to use, ‘hg19’ or ‘hg38’.

• refdir: reference folder for aligner (bowtie2 or bismark).

• outdir: Overall result folder.

• data: data type, ‘WGBS’ or ‘WGS’.

• type: data type, ‘paired’ or ‘single’.

• JavaMem: Java memory for every thred, “10G” like.

• case: case NAME for creating case specific folder.

• ctrl: control NAME for creating control specific folder.

Example usage:

from cfDNApipe import *

pipeConfigure2(
    threads=20,
    genome="hg19",
    refdir=r"reference_genome/hg19",
    outdir=r"output/pcs_armCNV",
    data="WGS",
    type="paired",
    JavaMem="8G",
    case="cancer",
    ctrl="normal",
    build=True,
)