How To Run

1. Create a config file using the template, which takes the input samples along with general parameters, with a section defining the parameters, reference files, and resources configurations for each run and each pipeline. See configuration for details on available options and configurations.

2. Create an input.csv or an input.yaml file (following the descriptions here) to provide input files for each sample. If using an input CSV, add the path to the CSV to the config generated in step 1.

3. Launch the pipeline using:

# YAML input
nextflow run \
    /path/to/metapipeline-dna/main.nf \
    -c /path/to/generated/config \
    -params-file /path/to/generated/input.yaml

# CSV input
nextflow run \
    /path/to/metapipeline-dna/main.nf \
    -c /path/to/generated/config

Note: UCLAHS-CDS users, submit the pipeline using the submission script.

warning: A low-resource partition (e.g F2 with 2 CPUs and 4GB of memory) is sufficient for the leading job.

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