pipeline
pipeline
Helpers for bioinformatics pipelines
Submodules:
Main classes & functions
count_pipeline_samples: Count the number of samples in a pipeline run.Pipeline: Base class for all pipelines.create_pipeline: Create a pipeline object from a pipeline name.
Functions
| Name | Description |
|---|---|
| count_pipeline_samples | Count the number of samples in a pipeline run. |
| create_pipeline | Retrieves a pipeline class by its name from the provided pipelines dictionary. |
count_pipeline_samples
pipeline.count_pipeline_samples(tree_str, pipeline_name)Count the number of samples in a pipeline run.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
| tree_str | str | The tree as a JSON string representing the pipeline run output directory (from tree -aJ command). |
required |
| pipeline_name | str | The name of the pipeline. | required |
Returns
| Name | Type | Description |
|---|---|---|
| int | The number of samples in the pipeline run. Returns NaN if the pipeline is not recognized. | |
| list | The sample names in the pipeline run. Returns an empty list if the pipeline is not recognized. |
See Also
~ccbr_tools.spooker.get_tree: The function used to generate the tree structure.
create_pipeline
pipeline.create_pipeline(pipeline_name, pipelines=PIPELINES)Retrieves a pipeline class by its name from the provided pipelines dictionary. Args: pipeline_name (str): The name of the pipeline to retrieve. pipelines (dict, optional): A dictionary mapping pipeline names to pipeline functions or objects. Defaults to PIPELINES. Returns: object or None: The pipeline class if found; otherwise, None.