RNAseq-alignment/README.md

# RNA Sequencing Alignment Pipeline

> Author:  Li Zhihuil; Qingwang Chen
>
> E-mail：qwchen20@fudan.edu.cn
>
> Git: http://choppy.3steps.cn/renluyao/RNAseq_germline_datapotal.git
>
> Last Updates: 2020/12/02

# 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/RNAseq-alignment
# 非第一次安装
```
$ choppy install chenqingwang/RNAseq-alignment -f 

# 查询已安装APP
```
$ choppy apps

# Quick Start
```
# 准备 samples.csv 文件
$ choppy samples chenqingwang/RNAseq-alignment-latest > samples.csv
# 准备无默认参数的samples.csv 文件
choppy samples --no-default chenqingwang/RNAseq-alignment-latest > samples.csv

# 提交任务
$ choppy batch chenqingwang/RNAseq-alignment-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/