cbcga-wes-qc

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README.md

Author: Yaqing Liu

Email: yaqing.liu@outlook.com

Last Updates: 23/04/2021

Requirements

choppy
Ali-Cloud
Linux

Introduction

This APP is used to

convert a FASTQ file to an aligned BAM file.
QC the data at the level of FASTQ and BAM, based on FastQC, FastQ Screen and Qualimap.

Please carefully check the reference genome, bed file, etc.

Usage

open-choppy-env

choppy install YaqingLiu/cbcga-wes-qc-latest

choppy samples YaqingLiu/cbcga-wes-qc-latest --no-default
# sample_id,fastq_1,fastq_2

choppy batch YaqingLiu/cbcga-wes-qc-latest samples.csv -p Project -l Label

# Query the status of all tasks in the project
choppy query -L Label | grep "status"