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 --project-name Your_project_name

Input File

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

{
  "fq": [
    "oss://choppy-cromwell-result/test-choppy/..._lane1_1.fq.gz",
    "oss://choppy-cromwell-result/test-choppy/..._lane2_1.fq.gz",
    "oss://choppy-cromwell-result/test-choppy/..._lane3_1.fq.gz"
  ],
  "panel_id": "test_1.fq.gz",
  "sample_id": "test_1.fq.gz"
}