New User Guide

[maotian06]

1. Installation

First install the nftest in the cluster:

pip install git+ssh://[email protected]/uclahs-cds/tool-NF-test.git

If any branch is needed, using:

pip install git+ssh://[email protected]/uclahs-cds/tool-NF-test.git@branch-name

To check if the nftest is installed, run

nftest -h

The output should be:

usage: nf-test [-h] [-V] [CONFIG] {init} ...

positional arguments:
  CONFIG         Path the the nextflow test config YAML file. If not given, it looks for nf-test.yaml or nf-test.yml
  {init}
    init         Initialize nftest.

optional arguments:
  -h, --help     show this help message and exit
  -V, --version  Version

2. Set up the initial test case

To set up a simple test case, first, spin a F32 or a F72 node, and change the directory to a pipeline directory.

Then run the following command to initiate the test folder.

nftest init

It will create one nftest.yml file under the current directory and a test folder with a global.config inside.

Open the nftest.yml , there will be two sections, global and cases. No change is needed for the global section. For the case section, write the specific pipeline input, here is an example:

cases:
  - name: test-multi-sample
    message: running nftest on development branch of call-sSNV
    skip: false
    nf_script: pipeline/call-sSNV.nf
    nf_config: test/test_mutect2/test_multi_tumor/test-tumor.config
    params_file: test/test_mutect2/test_multi_tumor/test-multi-tumor.yaml
    verbose: true

Then run the following command nftest. The test should start in the terminal.