catreads/README.md

Author: Jun Shang Email: shangjunv@163.com Last Updates: 10/05/2022

Requirements

• choppy
• Ali-Cloud

# Activate choppy environment
$ open-choppy-env

# Install app
$ choppy install junshang/catreads

# Create input file `samples.json`
touch samples.json

quick start

$ choppy batch junshang/catreads-latest sample.json -p Your_project_name

Input File

Input file samples.json should be in the form of json. For example:

{
  "fqs": [
    "oss://choppy-app-example-data/RNAseq/fastq_1m_reads/tumor_1M_1_R1.fq.gz",
    "oss://choppy-app-example-data/RNAseq/test_fq/test_R1.fq.gz"
  ],
  "sample_name": "test_1.fq.gz",
  "sample_id": "test_1",
  "disk_size": 200
}