4. NCBI

Running NCBI workflow¶

1. sarscov2 workflow has been completed (see Analysis for more details)
2. gisaid workflow has been completed (see GISAID for more details)
3. Change working directory to the analysis pipeline directory

4. Run analysis workflow

   • There are several subworkflows that are available to the user. These include:

     • INPUT:

       • Transforms passing samples metadata into NCBI required template(s) (NOTE: several batches may be created dependent on file size)
       • Transforms passing samples FASTA files into NCBI required FASTA (NOTE: several batches may be created dependent on file size)

     • OUTPUT:

       • Merge NCBI ID's into final output report

#1 change to the working directory
cd SARS_CoV_2_Workflow

#2A run workflow command: ncbi; subworkflow INPUT
bash run_analysis_pipeline.sh -p gisaid -n name_of_project -s input

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