README.md

Methods

To use a common align_methods function:

• In the pipeline-specific methods.config, include the align_methods.config
• Use any of the available functions as needed

Available functions

• set_params_from_input - Function to extract parameters from a CSV input and format it into a YAML-like list of maps with each map corresponding to one FASTQ file/pair; the inputs are loaded under params.input.FASTQ; generally should be called in the pipeline's methods.set_up() function; should be called before any parameter validation

Example

Set Params from Input

includeConfig "/path/to/align_methods.config"
...
methods {
    ...
    set_up = {
        ...
        align_methods.set_params_from_input()
        schema.load_custom_types("/path/to/custom_schema_types.config")
        schema.validate()
    }
}

Custom schema types

• InputNamespace: Used for align-DNA and -RNA inputs; Check that input is namespace of expected types
• ListFASTQPairs: Used for input FASTQ list; Check that input is list of namespace of expected types

References