How To Run

Requirements: Currently supported Nextflow versions: 23.04.2

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 (Template YAMLs).

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

4. YAML input

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

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