chenqingwang/rmats: For RNA-seq data, from bam/fastq to AS sites files.

For RNA-seq data, from bam/fastq to AS sites files.

chenqingwang fa679c0d65 更新 'tasks/rmats.wdl'		vor 4 Jahren
demo_samples	上传文件至 'demo_samples'	vor 4 Jahren
tasks	更新 'tasks/rmats.wdl'	vor 4 Jahren
README.md	更新 'README.md'	vor 4 Jahren
defaults	更新 'defaults'	vor 4 Jahren
inputs	first commit	vor 4 Jahren
workflow.wdl	更新 'workflow.wdl'	vor 4 Jahren

README.md

Author: Qingwang Chen

Email: qwch20@fudan.edu.cn

Last Updates: 25/03/2021

Requirements

choppy
Ali-Cloud
Linux

# 激活choppy环境
$ source activate choppy (open-choppy-env)

# 第一次安装
$ choppy install chenqingwang/rmats:v4.1.1
# 非第一次安装
$ choppy install chenqingwang/rmats:v4.1.1 -f 

# 查询已安装APP
$ choppy apps

Quick Start

# 准备 samples.csv 文件
$ choppy samples chenqingwang/rmats-v4.1.1 > samples.csv
# 准备无默认参数的samples.csv 文件
choppy samples --no-default chenqingwang/rmats-v4.1.1 > samples.csv

# 提交任务
$ choppy batch chenqingwang/rmats-v4.1.1 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/