CWL Definition files for Bioinformatics NGS data analysis

Requirements

Python 3.x
CWLtool
Node.JS
Conda (Bioconda) or Docker

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

With the exception of certain third-party files summarized below, 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 the authors in any work or product based on this material.

mitsuhashi/cwl-ngs-workflows-cbb