CWL Definition files for Bioinformatics NGS data analysis
Requirements
CWL Tools
Defined in folder tools
CWL Workflows
Defined in workflows
Conda execution
Install and configure Conda and Bioconda
Creating a ~/.condarc file
Create a .condarc in your home directory and add:
channels:
- conda-forge
- bioconda
- defaults
ssl_verify: true
Bioconda environment cwltool
Creating a conda environment
conda create -n cwltool
Installing the packages
conda install -n cwltool cwltool nodejs
Activating the cwltool env
conda activate cwltool
Then, all the required programs and tools will be available in the user $PATH
Running cwltool
Using Conda as runtime environment the cwltool should be executed with the following examples:
cwltool --no-container --beta-conda-dependencies --beta-dependencies-directory /path-to-directory/storing-conda-envs
Docker execution
Execute cwltool with these options if Docker is installed and user has permissions to pull images:
cwltool --no-read-only --beta-use-biocontainers
Public Domain notice
National Center for Biotechnology Information.
This software is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the authors' official duties as United States Government employees and thus cannot be copyrighted. This software is freely available to the public for use. The National Library of Medicine and the U.S. Government have not placed any restriction on its use or reproduction.
Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the NLM and the U.S. Government do not and cannot warrant the performance or results that may be obtained by using this software or data. The NLM and the U.S. Government disclaim all warranties, express or implied, including warranties of performance, merchantability or fitness for any particular purpose.
Please cite NCBI in any work or product based on this material.