How To Run

The pipeline is currently configured to run on a SINGLE NODE mode with normal only, tumor only, normal-tumor paired, or multiple normal and tumor samples.

1. Update the params section of the .config file (Example config).

2. Update the YAML.

3. Download the submission script (submit_nextflow_pipeline.py) from here, and submit your pipeline below.

Note: Because this pipeline uses an image stored in the GitHub Container Registry, you must follow the steps listed in the Docker Introduction on Confluence to set up a PAT for your GitHub account and log into the registry on the cluster before running this pipeline.

• YAML input

python submit_nextflow_pipeline.py \
       --nextflow_script /path/to/main.nf \
       --nextflow_config /path/to/call-gSNP.config \
       --nextflow_yaml /path/to/sample.yaml \
       --pipeline_run_name job_name \
       --partition_type <type> \
       --email email_address

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