2. Analysis

Running Analysis workflow¶

1. Initialization has been complete (see Getting Started for details)
2. Change working directory to the analysis pipeline directory
3. Run analysis workflow
   • There are several subworkflows that are available to the user. These include:
     • DOWNLOAD: Downloads analysis files for processing directly from BASESPACE
     • BATCH: Creates sample batches dependent on project size and input from config_pipeline.yaml
     • ANALYZE: Processes batches individually, including:
       • Downloads raw data (FASTA) and quality control files from BASESPACE
       • Submits batch to staphb-wf cecret workflow
       • Transforms results into batch level analysis and quality control reports
     • REPORT: Merges batch outputs into final analysis and quality control reports
     • CLEAN: Removes intermediate files, and working directories
     • ALL: Runs all of the above steps, sequentially

#1 change to the working directory
cd SARS_CoV_2_Workflow

#2A run workflow command: sarscov2
bash run_analysis_pipeline.sh -p sarscov2 -n name_of_project

#2B run workflow command: sarscov2; subworkflow DOWNLOAD
bash run_analysis_pipeline.sh -p sarscov2 -n name_of_project -s DOWNLOAD