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Background

The ODHL SARS-COV2 pipeline should be deployed, as follows:

Overview

The pipeline workflow is as follows: - Initialize - SARSCOV2 Analysis - GISAID Upload - NCBI Upload Preparation

Usage

  1. Change working directory to the analysis pipeline directory
  2. Initialize the pipeline
  3. Run sarscov2 analysis workflow
  4. Add metadata manifest to /name_of_project/logs/manifests dir
  5. Run gisaid workflow
  6. Move /name_of_project/ dir to the L:Drive
  7. Run ncbi workflow; subworkflow input
  8. Upload NCBI files to NCBI offline
  9. Add NCBI upload results files to /name_of_project/logs/ncbi dir
  10. Run ncbi workflow; subworkflow output
#1 Change working directory to the analysis pipeline directory
cd SARS_CoV_2_Workflow

#2 Initialize the pipeline
bash run_analysis_pipeline.sh -p init -n name_of_project

#3  Run `sarscov2` analysis workflow
bash run_analysis_pipeline.sh -p sarscov2 -n name_of_project -s ALL

#4 Add metadata manifest to `/name_of_project/logs/manifests` dir
# done via an SSH connection

#5  Run `gisaid` workflow
bash run_analysis_pipeline.sh -p gisaid -n name_of_project -s ALL

#6 Move `/name_of_project/` dir to the L:Drive
# done via an SSH connection

#7 Run `ncbi` workflow; subworkflow `input`
bash run_analysis_pipeline.sh -p ncbi -n name_of_project -s input

#8 Add NCBI files to L:Drive; Upload NCBI files to NCBI offline
# done via an SSH connection

#9 Add NCBI upload results files to `/name_of_project/logs/ncbi` dir
# done via an SSH connection

#10 Run `ncbi` workflow; subworkflow `output`
bash run_analysis_pipeline.sh -p ncbi -n name_of_project -s output
Last update: 2023-11-15