https://github.com/ncbi/cwl-ngs-workflows-cbb
A set of CWL tools and workflows used by NCBI Computational Biology Branch for NGS data analysis
https://github.com/ncbi/cwl-ngs-workflows-cbb
cwl-workflow ngs ngs-analysis ngs-pipeline
Last synced: 2 months ago
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A set of CWL tools and workflows used by NCBI Computational Biology Branch for NGS data analysis
- Host: GitHub
- URL: https://github.com/ncbi/cwl-ngs-workflows-cbb
- Owner: ncbi
- License: other
- Created: 2019-06-14T19:56:21.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2023-06-29T15:42:03.000Z (over 2 years ago)
- Last Synced: 2025-06-09T00:41:14.506Z (4 months ago)
- Topics: cwl-workflow, ngs, ngs-analysis, ngs-pipeline
- Language: Common Workflow Language
- Size: 629 KB
- Stars: 23
- Watchers: 10
- Forks: 10
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# CWL Definition files for Bioinformatics NGS data analysis
## Requirements
* Python 3.x
* [CWLtool](https://github.com/common-workflow-language/cwltool)
* Node.JS
* Conda ([Bioconda](https://bioconda.github.io/)) or Docker
## CWL Tools
Defined in folder *tools*
## CWL Workflows
Defined in *workflows*
## Conda execution
Install and configure Conda and [Bioconda](https://bioconda.github.io/)
### 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.