CWL-CommandLineTools

UMCU Genetics CWL CommandLineTools

Getting started with CWL

• CWL User Guide
• CWL tutorial using SNPEFF

CWL Workflows

Put uri to our workflows here.

Contributing

We invite anybody to contribute to the UMCU Genetics CWL CommandLineTools repository. If you would like to contribute please use the following procedure:

• Fork the repository
• Commit the changes to your fork
• Submit a pull request

The pull request will be reviewed and included as fast as possible.

Contributing guidelines

• Use the tool/version/subtool folder structure of this repository.
• Use CamelCase for tool names
• Use the original tool version numbering
• Use tool option names for optional inputs and outputs.
• Use lowercase with words separated by underscores for positional inputs and outputs.
• All input and output identifiers should reflect their conceptual identity. Use informative names like unaligned_sequences, reference_genome, phylogeny, or aligned_sequences instead of foo_input, foo_file, result, input, output, and so forth.
• Mark all input and output Files that are read from or written to in a streaming compatible way (only once, no random-access), as streamable: true.
• Include a top level short label summarising the tool/workflow.
• If useful, include a top level doc as well. This should provide a longer, more detailed description than was provided in the top level label.
• Use type: enum instead of type: string for elements with a fixed list of valid values.