Read Filtering Workflow

The read_filtering workflow uses fastq and trimmomatic to assess the quality of sequencer reads and filter out low-quality reads.

The user has control over the names and URLs of sequence data that is downloaded, as well as parameters like the quality threshold.

Quick Start

To list available workflows (only one):

$ taco ls

To get rules defined by the workflow:

$ taco ls read_filtering

To run the workflow using the provided workflow config and parameter files,

$ taco read_filtering \
    --config-yaml=workflow-config/config_step1.yaml \
    --params-yaml=workflow-params/config_step1.yaml

By default, this will generate output files in the data/ directory. To change the output directory, use the --prefix flag:

$ taco --prefix=my_data read_filtering \
    --config-yaml=workflow-config/config_step1.yaml \
    --params-yaml=workflow-params/config_step1.yaml

If the directory does not exist, it will be created.

Continue reading for more details about how to determine what rules a workflow defines, how to set parameters for the read filtering workflow, and the various target files that are useful for the workflow config file.