pipeConfigure

This function is used for setting Configures.

Parameters

pipeConfigure(threads=(cpu_count() / 2), genome=None,
              refdir=None, outdir=None, data=None,
              type=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, must be ‘hg19’ or ‘hg38’.

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

• outdir: Overall result folder, it usually contains tmpdir, finaldir and repdir.

• data: Input data type, ‘WGBS’ or ‘WGS’.

• type: Input sequencing type, ‘paired’ or ‘single’.

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

• build: Whether checking reference and building reference once not detect.

Example usage:

from cfDNApipe import *
import glob

pipeConfigure(
    threads=60,
    genome="hg19",
    refdir=r"path_to_reference/hg19",
    outdir=r"path_to_output/snv_output",
    data="WGS",
    type="paired",
    build=True,
    JavaMem="10G",
)