Configure2

This function is used for setting all the pipe configures.

Note

Configure or Configure2 should be called before analysis.

Parameters

# get configure names
Configure2.getConfigs()

# get configure through name
Cinfigure2.getConfig(key)

# set configure through name
Cinfigure2.setConfig(key, val)

# additional function: check virus genome
Configure2.virusGenomeCheck(folder=None, build=False)

# additional function: check SNV reference
Configure2.snvRefCheck(folder=None, build=False)

• key, val: key and value.

• folder: folder path to the virus genome or snv genome files.

• build: download and build by cfDNApipe or not.

Example usage:

from cfDNApipe import *

pipeConfigure2(
    threads=60,
    genome="hg19",
    refdir="path_to_genome/hg19_bowtie2",
    outdir="path_to_output/pipeline-WGS-comp",
    data="WGS",
    type="paired",
    JavaMem="8G",
    case="cancer",
    ctrl="normal",
    build=True,
)

Configure2.getConfigs()

Cinfigure2.getConfig("genome")