fastp_suppa2/README.md

README.md
Author: Qingwang Chen; Chenglin Liu

Email: qwch20@fudan.edu.cn

Last Updates: 17/01/2022

Brief Introduction
For RNA-seq data, from bams to AS Information files.

Requirements
choppy
Ali-Cloud
Linux
# 激活choppy环境
$ source activate choppy (open-choppy-env)

# 第一次安装
$ choppy install chenqingwang/fastp_suppa2
# 非第一次安装
$ choppy install chenqingwang/fastp_suppa2 -f 

# 查询已安装APP
$ choppy apps
Quick Start
# 准备 samples.csv 文件
$ choppy samples chenqingwang/fastp_suppa2-latest > samples.csv
# 准备无默认参数的samples.csv 文件
choppy samples --no-default chenqingwang/fastp_suppa2-latest > samples.csv

# 提交任务
$ choppy batch chenqingwang/fastp_suppa2-latest samples.csv -p Your_project_name -l Your_label

# 查询任务运行状况
$ choppy query -L Your_label | grep "status"

# 查询失败任务
$ choppy search -s Failed -p Your_project_name -u chenqingwang --short-format

# 结果文件地址
$ oss://choppy-cromwell-result/test-choppy/Your_project_name/