How To Run

Below is a summary of how to run the pipeline. See here for more information on running Nextflow pipelines.

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.

1. The recommended way of running the pipeline is to directly use the source code located here: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/release/, rather than cloning a copy of the pipeline.

2. The source code should never be modified when running our pipelines

3. Copy and edit the input config file

Make sure the reference .fa file in config file matches the reference genome in the input BAM files.

1. Copy and edit the input YAML
2. The pipeline can be executed locally using the command below:

nextflow run path/to/main.nf -config path/to/input.config -params-file input.yaml`

For example,

• path/to/main.nf could be: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/release/5.0.0/main.nf
• path/to/input.config is the path to where you saved your project-specific copy of template.config
• path/to/input.yaml is the path to where you saved your project-specific copy of template.yaml

To submit to UCLAHS-CDS's Azure cloud, use the submission script here with the command below:

python path/to/submit_nextflow_pipeline.py \
    --nextflow_script path/to/main.nf \
    --nextflow_config path/to/input.config\
    --nextflow_yaml path/to/input.yaml \
    --pipeline_run_name <run_name> \
    --partition_type F72 \
    --email jdoe@ucla.edu

Note: Although --partition_type F2 is an available option for small data sets, Mutect2 and Muse will fail due to lack of memory.

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