Getting Started

  1. Dependencies
  2. Nextflow Basics
    1. Specifying the workflow version
    2. Specifying resource limits
    3. Resuming a run
  3. Testing EPITOME
  4. Basic Usage

Dependencies

EPITOME is built using Nextflow. Nextflow simplifies the development and execution of complex, scalable data analysis workflows by enabling reproducibility, portability across computing environments, and seamless integration with container technologies like Docker and Singularity.

The following are required to run EPITOME:

EPITOME does not support Conda / Mamba. Please submit a feature request if this is essential for your lab.

Nextflow Basics

Below are some general pointers for how to run Nextflow workflows.

Specifying the workflow version

There are two general ways you can specify which version of EPITOME you want to run:

  1. Tell Nextflow which version you want to use

     nextflow run doh-jdj0303/EPITOME \
     -r v1.0 \
     -profile docker \
     --input samplesheet.csv \
     --outdir results

  2. Clone the workflow version manually

     git clone https://github.com/doh-jdj0303/EPITOME.git -b v1.0 

     nextflow run EPITOME/main.nf \
     -profile docker \
     --input samplesheet.csv \
     --outdir results

Nextflow caches repos in ~/.nextflow/assets/ by default. Removing this cache can be helpful when running into version-related issues.

Specifying resource limits

We recommend adjusting the maximum resource limits that Nextflow can use. Setting these limits too high will cause the workflow to fail. There are four general ways to achieve this:

  1. Set limits via command-line parameters 
     nextflow run doh-jdj0303/EPITOME \
     -r v2.0 \
     -profile docker \
     --input samplesheet.csv \
     --outdir results \
     --max_cpus 8 \
     --max_memory 12.GB
  2. Set limits in the nextflow.config config file 
         // Max resource options
     // Defaults only, expecting to be overwritten
     max_memory                 = '128.GB'
     max_cpus                   = 16
     max_time                   = '240.h'
  3. Set limits via a custom config file custom.config 
     process {
 // Default maximum resources allowed per process
 withName: '*' {
     maxCpus = 16         // set your desired max CPUs
     maxMemory = '64 GB'  // set your desired max memory
 }
 }

     nextflow run doh-jdj0303/EPITOME \
     -r v2.0 \
     -c custom.config \
     -profile docker \
     --input samplesheet.csv \
     --outdir results

All parameters can be supplied via a custom config file, including input and outdir. This is generally best practice and should be used when possible.

Resuming a run

Nextflow can resume a run. This comes in handy when a workflow fails or when you need to make small parameter adjustments. Below is an example of how you can resume a workflow run:

nextflow run doh-jdj0303/EPITOME \
    -r v2.0 \
    -profile docker \
    --input samplesheet.csv \
    --outdir results \
    -resume

Testing EPITOME

Verify that EPITOME is running properly using the command below. Update -profile to your preferred container engine.

nextflow run doh-jdj0303/EPITOME \
    -r v2.0 \
    -profile (docker|podman|apptainer|singularity),test \
    --outdir EPITOME_test

You can learn more about how the test configuration here

Basic Usage

In-depth overviews of inputs and outputs are available. All other questions / issues should be submitted via the EPITOME GitHub issues page or by email.