3. GISAID

Running GISAID workflow¶

1. sarscov2 workflow has been completed (see Analysis for more 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:

     • PREP:

       • Perform QC for samples that fail N threshold, files added to failed list
       • Perform QC for samples missing metadata files, files added to failed list
       • Transforms passing samples metadata into GISAID required template
       • Transforms passing samples FASTA files into GISAID required FASTA

     • UPLOAD:

       • Uploaded metadata and FASTA files to GISAID

     • QC:

       • Merge GISAID ID's into final output report
       • Moves FASTA files to appropriate final directories (IE gisaid_complete)

     • ALL: Runs all of the above steps, sequentially

#1 change to the working directory
cd SARS_CoV_2_Workflow

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

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