witsGWAS cheat sheet

Cheat Sheet

witsGWAS is a simple human GWAS analysis workflow for data quality control (QC) and basic association testing.

It was built using the Ruffus python library and employs the Rubra pipeline system for bioinformatics workflows to run tasks/jobs on a distributed computer cluster.

1. Visualizing and running pipelines

see Guide or type rubra -h at the unix prompt

Action	Syntax
generate pipeline flowchart	rubra pipeline_name.py --config pipeline_name_config.py pipeline_name_stages_config.py PipelineUserInput.py --style flowchart
generate pipeline printout	rubra pipeline_name.py --config pipeline_name_config.py pipeline_name_stages_config.py PipelineUserInput.py --style printout
run pipeline	rubra pipeline_name.py --config pipeline_name_config.py pipeline_name_stages_config.py PipelineUserInput.py --style run
repeat tasks	rubra pipeline_name.py --config pipeline_name_config.py pipeline_name_stages_config.py PipelineUserInput.py --force 'task_name' --style run
run part of the pipeline	rubra pipeline_name.py --config pipeline_name_config.py pipeline_name_stages_config.py PipelineUserInput.py --end 'task_name' --style run

2. Interrupting pipeline runs

see Guide

Action	Syntax
stop pipeline run	ctrl -c